The short answer is no, Patrick did not commit atrocities against pagans. There is absolutely no evidence for this.

The information we have on Patrick come from his own writings - two documents, his Confession [which is an autobiography] and a later letter that he wrote to a British bounty hunter, in which Patrick rails against the bad treatment of the Irish from this apparent hunter from abroad. His Confession details Patrick's own captivity into slavery, his early time in Ireland as a slave and his escape and return to Ireland as a missionary.

The other stories on Patrick are invented propaganda from a much later time. The stories of fighting druids, lighting fires on hills to confront pagans etc. are pure invention. The snakes is an even later invention as is the shamrock iconography.

One notable aspect of the conversion of the Irish to Christianity is that there are no martyrs. It was a peaceful transition and a large part of the pagan religion got easily incorporated into early Irish Christianity.

You might be interested in this thread from a few years ago: A girl I know gets indigant every St. Patricks Day, because she believes that St. Patrick conquered Ireland and forcibly converted them, committing genocide against the Pagan druids who lived there. Is this claim accurate? If so, to what extent?

It contains some good information from /u/Lonbeimnech and /u/depanneur on the subject.