What exactly would the rabbits have eaten if Wallace successfully conditioned them to not eat vegetables? Would they have just starved to death?
Rabbits are also known to eat grass and hay, so it's unlikely.
Based on some of the Were-Rabbit behavior, specifically at the end when he got angry at Victor Quartermaine hurting Lady Tottington and how he recognizes Gromit, there is a chance that it's a Superpowered Evil Side for Wallace at best where he loses himself to his rabbit's instinct or at worst an And I Must Scream situation where he could see and know everything that happens around him yet can't do anything until he fought back against it.
It could just be that he gained a degree of awareness of himself in that state after he learned what was happening to him, whereas before he was unaware of the change.
When Victor left Tottington Hall near the beginning, he had a rabbit on his head that he mistook for his wig. However, when we see him next at the church meeting, he has an identical wig and the rabbit is nowhere to be seen. Considering that he originally wanted to shoot the rabbits dead, it's not too far fetched to guess that he killed the rabbit on his head when he found out about it.
Alternatively, he could have just gone back for the wig, particularly when he was still trying to appeal to Lady Tottington.
When Victor challenges Wallace to hand-to-hand combat he insists that they follow "Queensberry Rules", a traditional set of rules for boxing, one of which is "no rabbit punches" (a blow to the back of the head).