Allow her to train anyway. If she’s used to running on three legs, she should have no trouble on the battlefield. Just be aware that, yes, you will have to take into consideration the fact that she may not do things the same way as fully able-bodied eevee do. Be aware of how she uses her body normally and construct training regimens to accommodate her disability. Consider also teaching her a few distance moves (such as Shadow Ball and Swift) that she can use if she pushes herself too hard with physical moves.
If she seems like she’s struggling on just three legs, it might also be worth it to look into obtaining a prosthetic for her. There are certain companies out there—Silph, for example—that can make 3D-printed pokémon prosthetics which are actually quite inexpensive.
Best of luck to you and your eevee, anonymous!