To me, it feels like they've pretty much jumped the rails and smashed them beyond repair. Even if they explain away the whole hair color thing, there's still far too many changes (particularly Alicia's personality shift, which I personally despise) for it to resemble the game again.
Not that I don't understand changing things. After all, when you get down to it, Valkyria Chronicles doesn't have a huge amount of plot. You have to add and change things somewhere, particularly if you want to keep dramatic tension about Welkin and Alicia ending up together (it's obvious even at the start of the game, not that that really matters; it wasn't the focus, after all). I just object to the way that they're doing it. Personally, I think the manga is doing a great job of reinterpeting the game, and gives me what I really wanted out of VC in other media: expansion on the other characters.
Probably the most apparent example of this is...
tl;dr : The manga is doing a better job with its changes.