The Flash Universe isn't done with Harrison Wells just yet.
In the latest Entertainment Weekly Spoiler Room piece, the question was asked whether Barry's actions at the end of the season finale would result in Tom Cavanagh making an exit from the show going forward. According to EW's source's that is not the case.
"Details on next season are being kept tightly under wraps, but I can tell you that Tom Cavanagh will be back as a series regular for season 3. Consider this: If the show does indeed move forward with Flashpoint, then the Reverse-Flash never killed Earth-1 Harrison Wells and his wife, meaning we could see the original Wells next season. Maybe. Hopefully".
The current Harrison Wells and Jesse are seen returning to Earth-2 by season's end, but if Cavanagh is indeed still part of the cast, that could mean a few things. Either we will be seeing more Earth-2 content interspersed throughout the season, or the two characters could play an important role in fixing the timeline, now that Barry's gone and messed it all up. Either way, more Cavanagh is a good thing no matter how you slice it.
DC is keeping details to a minimum, but it appears that we might be getting a Flashpoint-centric storyline in Season 3, as Barry presumably screws up the timeline a great deal by saving his mother from Reverse Flash, something he didn't do in a previous episode. By episode's end, we also see Hunter Zolomon carried off and possibly turned into the Black Flash.