Pliny the Younger's not being Christian has not prevented Christians from reading his work, nor have Christians only been interested in classical texts on topics that relate to Christianity (though it has certainly affected how they've read many texts). There was a good AskHistorians answer written about this not too long ago which I can't find a link to now but essentially, Christian scholars did not systematically avoid studying pre-Christian Roman texts, not in medieval times or in Renaissance times or in early modern times. That's why we have classical literature at all: because medieval Christians created and copied manuscripts of authors like Pliny.

Pliny's account of the eruption of Vesuvius comes from his Epistles, a collection of personal letters addressed to various recipients. Today, these epistles (as is also the case with the other classical Roman epistles we have, written by Cicero) are mostly of interest to historians, especially social historians: people use them as evidence for Roman elite social networks and their concepts of politeness and hierarchy, for the inner workings of the Roman imperial administration as exemplified by the communications between Pliny (the governor of the province of Bithynia) and Emperor Trajan, for (as you say) Trajan's policy toward Christians, for literary and philosophical discourses in Pliny's circle, and other topics like that.

The way that modern scholars focus on the historical details, though, is not how it's always been, so let's go back to the beginning of the history of readership. Although the Epistles are generally thought to have been arranged, and perhaps written, with public publication in mind, they were not very popular in antiquity (we can tell because only a couple of other ancient authors quoted or referenced them). From the late 4th century on, as part of a revived interest in "Silver Age" Latin literature, Pliny's Epistles became somewhat better known. A few authors published books of letters which were clearly inspired by Pliny: Symmachus, Ambrose, and (a century later) Sidonius Apollinaris. The influence of Pliny on these works was mostly one of form (just the concept of publishing one's books of letters), but Sidonius in particular also quoted Pliny extensively and took stylistic inspiration from him. So we might say that in late antiquity, Pliny was read as a literary stylist and as the most direct inspiration for an epistolary genre.

In the middle ages, that epistolary genre dwindled and Pliny became unpopular again. A lot of Roman texts were widely taught in medieval schools, but Pliny's epistles were not. Starting in the Renaissance, though, Pliny was read much more. The presentation of character is an important topic in both the literary and historical interpretation of the Epistles: he presents himself as an idealized country gentleman, trying his best to be a good man under some bad emperors, and his uncle (Pliny the Elder) as a devoted scholar who he sought to emulate. So to European writers of the Renaissance and early modern period, Pliny's primary value was as a model of how to behave and write with tact, integrity, and intelligence, especially in a hierarchical court setting. (This coincided with the rediscovery of Pliny's letters to Trajan at the end of the 15th century.)

I hope I haven't gone off the rails too much talking about how Pliny was read in general. So what about Epistle 6.16 in particular, the one about Vesuvius? The excavations of Pompeii and Herculaneum certainly brought new attention and new context to Pliny's account, but people before that hadn't been totally ignorant of the geological phenomena he discussed. After all, Vesuvius still exists and still erupts and still has the same name: people who witnessed its various 17th and 18th century eruptions knew they were looking at the same volcano that Pliny wrote about. Epistle 6.16 was significant partly because the eruption killed Pliny the Elder, who was notable for his scientific observations.

Geographically, there's not much overlap between the archaeology and the letter. If you've read the letter, it's an account of Pliny the Elder and a group of his companions going toward Vesuvius to help a friend escape the eruption by boat. The only geographic places mentioned are Misenum (outside the area affected by the eruption), where the Plinies were living, and Stabiae, where the friend lived. There have been excavations at Stabiae. The various towns harmed or destroyed by Vesuvius were very much known to be real before they were rediscovered and excavated. None of them were especially significant towns, but they show up in ancient writings from time to time. So the excavations have added a huge amount of detail to what was known about the histories of those towns, but what was known about them didn't actually come from Pliny.

Bibliography

Latin Literature: A History, by Gian Biagio Conte.

Loeb Classical Library volumes 55 and 59. Pliny the Younger. Letters. 2 volumes, translated by Betty Radice