It is extremely hard to apply modern notions of war crimes like genocide to the pre-modern world. While there have existed behaviors that were condemned as outside the "normal" scope of war since time immemorial, there has rarely ever been an attempt to codify these taboos and enforce them across jurisdictional lines by third party arbitrators. To me, the idea of taking modern day ideas and applying them to events that happened over a millennia ago seems a little odd.

We can sit down and look at the definition of genocide as it stands today and try to determine if Charlemagne's actions constituted a genocidal campaign. However I think this is rather missing the point. Instead we should be examining contemporary reactions to try and get an idea of the situation, and how his actions were perceived by others and whether they violated the norms of battlefield conduct.

Indeed I think parallels can be drawn to other early Medieval events, even if there is quite a bit of time separating the two. What comes to mind immediately to me is the "Harrying the North" under William the Conqueror. While the two situations are not exactly comparable, there was no religious dimension to the Anglo-Saxon revolt in Northumbria for example (and this will be important later), it is still a useful comparison because it was unequivocally condemned by contemporary chroniclers as extremely excessive, damning, and gratuitous violence directed indiscriminately at the civilian population. I've written more about it here

So there does exist at least the idea of condemning the monarch's campaigns if they do go over the line into unnecessarily brutal.

Now is this the case for Clarlemagne's conquest? One one hand is extremely hard to say for sure since there are precious few sources from this time frame in general, and none from the pagan Saxon point of view. The only sources that do deal with the conquest of the Saxons directly come from an extremely biased Christian/Carolingian point of view.

In particular the sources available focus on the treachery of the Saxon rebels, who had supposedly expressed loyalty to Charlemagne and thus deserved their harsh treatment. Unrepentant pagans and serial rebels did not engender themselves to the Latin elite and their own writings.

So by the standards of the time, his conquests were not seen as particularly unduly brutal or harsh, in part due to the pagan nature of the Saxons that he was facing down. However, by the modern textbook definition, you could certainly say that he was engaging in genocide since he particularly targeted pagan practices and practitioners. I just do not think this is a useful metric to use when examining past societies.