She had brown hair in the flashbacks when she was Chris's partner in the BSAA. Here's a video of her from Mercenaries Mode:
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It was explained on a screen in the secret laboratory that Jill's cranial follicles changed pigmentation due to her being under statis in one of the big tubes.
The real reason Capcom did it was to keep her identity more of a mystery before the game game out. One of the early trailers ended with a blonde woman in a tube looking up. It would be too obvious that it was Jill if she had brunette hair, so they changed it to throw people off.
I'm willing to bet that if Jill stars in another Resident Evil game, she will return to her normal brunette self and it'll be explained away as a temporary side effect.