I always cut away the feet plastic thing that goes into the base (for small models), and for bigger models I cut away the pins of the feet. I paint the model first, then I make a really elaborate base, and glue the guys on the bases sometimes with repositioned feet. It would be better if you did cut him away and redid the base. (a few times I would do what you did, but then I would break the guys from bases, and that would break the bases in half, but you can still successfully fix them, and make your model look great.)
Ill show you an example
All 3 of those guys were glued into the slots, and their bases had sand carpets glued, foilage, stones, particles etc. but I still fixed them and made better bases. Also sorry for my mediocre painting job, I suxxors.