The theological ramifications of the rape of sworn virgins was a deeply troubling topic for male medieval ecclesiastics. The Latin Middle Ages inherited two traditions from antiquity. Champion of virginity Jerome wrote passionately that it was better for virgins to kill themselves than "let" themselves be raped. (And he was not alone in his stance.)

For Augustine, the unforgiveable sin of suicide was the worse end. He argued that true virginitas was a matter of will, with a physical manifestation, not a strictly corporeal matter. "The sanctity of the body," he wrote, "does not consist in the integrity of its members, nor in their exemption from all touch"--the body is sanctified by the purity of the will. The pollution of rape belongs to the one doing the polluting (the rapist).

But Augustine, man of his era, was not about to let women off the hook so easily, (ETA) as medieval interpreters saw it. Any sign of "positive" reaction from the woman--orgasm, not fighting, pregnancy--was taken as the lust of the body moving the will. So there was room for being raped to not cause sin. But not very much room.

Medieval theologians will side with Augustine over Jerome...but not very happily. Jane Tibbets Schulenberg's scrutiny of chronicle and hagiographic accounts of early medieval women is quite revealing. She finds examples of: lay women kidnapped into slavery/nonchaste life by barbarians, nuns killed by barbarians, and nuns who heroically disfigured themselves in an attempt to avoid being kidnapped for rape/concubinage. (Invariably, the nuns in these accounts are slaughtered instead, with no mention of rape by the chroniclers). Explicit references to holy women being raped are scanty and background, never being identified by place or name, generally one item in a catalog of marauding crimes used to envision the savagery of Vikings or southern raiders.

Thomas Aquinas, secure in his university position, followed Augustine over Jerome in his discussion of virginity, rape and suicide. For his rough contemporary Jacques de Vitry, "on the ground" as a traveling theologian, bishop, and champion of holy women, the issue was not so theoretical. Jacques wrote compassionately of the beguines (similar to nuns, but not attached to a formal monastic order) of Liege when the town was besieged and sacked in 1212. The beguines heroically threw themselves into sewers and the river to avoid rape (ahem...protect their chastity, thanks, Jacques). Fortunately--miraculously--none of them actually died! Theological crises of suicide and rape averted.

(Male) canon lawyers likewise agreed that virginity was a special status, specially threatened by rape. Church law repeatedly names the rape of virgins a worse crime/sin than raping married women or lay widows. (Although, as Ruth Mazo Karras notes, rape was rarely prosecuted in the Middle Ages due to the difficulty-bordering-on-impossibility of proving nonconsent). The 15C English poem Sir Gowther illustrates the inherent evil of its fathered by the devil protagonist in his rape and murder of nuns.

It's harder to excavate how nuns themselves perceived rape--the nebula of emotions churning around questions of vows, virginity, pollution, lust, shame, violation, and pain. Medieval nuns don't really write about it directly. While scholars today typically argue that male clerics made virginity a bigger deal than virgin women, it's not like chastity was unimportant as a vow. Hildegard of Bingen (12C) envisioned virginity as an existential state that sanctifies specifically women, a bedrock of her theological worldview. There is a lot of evidence to a widespread embrace of the idea of holy virgins as "brides of Christ," a self-identity that would have been enormously shadowed by rape.

And while we might be inclined to read with some skepticism Roger of Wendover's 13C account of 9C Abbess Ebba and her nuns gouging off their noses and lips to protect their chastity from Vikings (only to be burned alive by the furious, "spurned" ravagers), Jacques de Vitry's account of the Liege beguines would likely have been remembered by contemporary readers. It's impossible to retroactively determine the calculus of theological, social, and personal elements of medieval nuns' reaction to rape or the threat thereof, but it seems evident it was a topic of concern overall to women, on multiple levels, as well as male writers concerned almost exclusively with theology. 14-15C humanist Christine de Pisan went so far as to label rape and living with the aftermath "the greatest possible sorrow."

OP mentions Franciscan Second Order guidelines on claustration (cloister-making), which introduces a host of interrelated issues. It is a bog-standard topos of holy women's hagiographies that they flee to religious life when their parents are forcing them into marriage. Suitors visit convents to harass their potential-beloved inside. This issue was particularly pointed for the 13C (early) Franciscans, who wanted to be the religious order that only took people who really really wanted to be there--not people forced into monastic life by their wealthy, connection-seeking parents. (Every monastic order reform movement has this as a goal, to be clear.) How many of the stories in these vitae "really happened," and how many were just the necessary formula? It's impossible to tell--and maybe it doesn't matter. The idea and the fear were real, regardless of the immediacy of the threat.

An additional level of concern, although less discussed by male hagiographers, was the location of the mendicant (Franciscan, Dominican) houses: cities. It seems logical to me, at least, that jilted suitors were not the only male threat to a group of women living with just a few male servants nearby or confessors visiting some of the time. Margery Kempe in 15C Lynn, England (not in a convent) describes how she was scared to go alone to bed at night.

What is impossible to reconstruct, at least to my current knowledge, is the extent to which nuns themselves recognized forced sexual intercourse as rape versus the body forcing the will to give its consent. It seems most likely to me that medieval nuns would have shared in the general ethos of their time: that any sign of bodily response to rape, inability to fight off one's attacker, or the body's traitorous refusal to "shut that whole thing down" and still get pregnant from forced sexual intercourse meant that one's will had indeed consented and thus sinned. They lived in a culture in which it was not implausible to say suicide--a mortal, unforgiveable, hell-damning sin--was better than being raped.

Monastic disciplinary records and rules might seem surprisingly lenient towards nuns (and monks) denounced for sexual immorality--be it an affair with a local layperson or a case of rape. In addition to spiritual penance (bread and water meals, prayers, etc), there would likely be loss of rank privileges within the community. Removal from a convent office like chantress or mistress of novices, for example, or being forced to walk at the end of the line when the community processed into choir to sing the Divine Office. Would there have been community support for nuns who were raped? The images we have of community and friendships among sisters say yes. What did that support look like? Was it nuns trying to shore up the spiritual orientation and devotion to chastity of a fallen sister, or women commiserating about violation against one's will? Those questions are lost to the whispers of the past.

Christine de Pisan was a lay widow and a court writer, not a nun. Nevertheless, she is an explicit and explicitly female voice on rape from the late Middle Ages. Following Augustine and Jerome, she mentions suicide as one possible response to rape (displaying her classical education, her reference is the rape of Lucretia). Her bigger concerns, though, are what she sees as the other two possible reactions. Modern scholars have heralded more the exhortation to seek justice or vengeance for the rape (perhaps not surprisingly).

But the third response is perhaps of more interest in the case of cloistered nuns: grieving. Christine describes the aftermath of rape as a parallel to mourning, as for the death of a beloved. For medieval nuns who heard and read on a near-daily basis that they were the brides of Christ, whose sacramental vows to the Church may well have been professed in a wedding-like atmosphere, who were steeped in a culture of people who believed forced sexual intercourse almost certainly ended up as "consensual" instead of rape, mourning the death of their spotless marital relationship with Christ seems like it would have been a tragically common outcome.

Just a point of clarification, monastics, male or female, are not clergy. Some male monastics are ordained as clergy (priests, deacons, bishops), but no nuns (female monastics) are ordained.