First of all, the standard preface regarding the medieval world is again necessary: it is a very broad term, occupying about 1000 years worth. I assume you and your wife were discussing Medieval Western Europe, but even then there are differences depending on which area and which time frame we are discussing.

There have been previous discussions on this topic, but I would like to add a couple of points to that.

One cannot answer exactly how prevalent rape was (expanding on /u/801_chan's comment here) - putting a number on say 980's Denmark, 1250's England or 1490s Spain would probably be based around speculation. This is because records - both parish and otherwise - can be spotty, even with relatively well-documented people such as the peasant woman Christina Cok. You cannot say too much about her life, and that goes for especially medieval peasants.

I am afraid that I cannot answer the questions about the mental impact of rape either. This is before PTSD came to the forefront of public consciousness, and also, records for emotional trauma following rape is somewhat scarce compared to the actual crimes and punishments which were written down. I might be missing something, but I haven't found much of anything regarding emotional trauma following rape when studying this.

However, rape was prevalent enough for it to be considered a capital offense in many parts of Western Europe. It was however not followed in practice, as a study of the legal evidence from Venice around the Black Death years (1338 - 1358) show (This and the following is from McKay et. al 2008 p. 394-5)

This study will be of interest since rape was not practically considered a particularly serious crime against either victim or society, despite it being nominally a capital crime. The punishment did wary a bit: the rape of a noble, marriageable girl was either punished by the Venetian courts with either a fine or six months' imprisonment, while a non-noble or an already married woman would result in even lighter punishments.The reverse, that a non-noble would rape a noble, was severly penalized, as it was extremely rare.

One note that should be considered is that unmarried women who were not of noble birth were in many cases working as domestic servants, and they could be sent out on errands either alone or with male companions. Couple this with no real protection from society, and a noble youth could easily coerce or rape a non-noble. Noble women were more often secluded because of notions of female honor - like chivalry it did not exactly apply to the non-noble classes.

As for discussion of rape? Several notable men and women living at the time did indeed discuss the topic and its connotations, often with Christendom as their background:

Thomas Aquinas discussed rape in his Summa Theologica, where he considers rape a "specie of lust". Here it should be noted that Thomas tried to shape the Summa Theologica into a instruction book for moderate priests of the time, so a lot of concepts familiar to specialists of Roman history (such as the father being violated by the rape of his daughter in some cases) is present in the treatise.

Christine de Pizan, the woman that some scholars trace feminism's roots to, provides a different view. She completely rejected the accusation that women invite rape:

"Rest assured, dear friend, chaste ladies who live honestly take absolutely no pleasure in being raped. Indeed, rape is the greatest possible sorrow for them."

These two authors are not necessarily representative of medieval thought, but they should provide some inkling of the fact that while it was not prosecuted harshly, rape was still seen negatively by several key people.

I might've missed a lot of stuff, or done something completely wrong, but I hope I've helped this.

Sources:

McKay, et al: "History of Western Societies, 9th edition" printed in 2008 pages 394-395 and 404-405

Summa Theologica, by Thomas Aquinas: http://www.newadvent.org/summa/