40k RPG fluff is based, in large part, on tabletop fluff. On the tabletop, the Vindicare can 1-shot Land Raiders (or could in previous editions at least). FFG likely does not have the power to rewrite the existing fluff, which dictates the power of the Exitus and contributes to its fearsome tabletop rating.
Sure they can. FFG has been rewriting existing fluff all the time. The Vindicare himself is an example of this, considering that normally every single mission would have to be authorised by the High Lords of Terra, whereas here he's just added to the group as a permanent asset.
GW doesn't care as long as they keep to the most simple basics.
I think the people at FFG have already been rather clever about this, actually, by giving the Exitus rifle a rather sensible damage profile (2d10+2 Pen 5), with only the special Turbo Penetrator kicking it up to 4d10+2 Pen 9.
As a GM, I'd simply give a Vindicare only a single Turbo Penetrator, or a single clip of 10, and tell him to take good care of it as he won't get a replacement any time soon, forcing him to rely on the standard rounds for most enemies, and only breaking out the good stuff for critical assassinations. This way, I would not see a balancing problem with giving it a higher minimum damage.
Besides, is a maximum damage of 42 not a balancing concern already? The current profile only means the result will be highly random, fluctuating between "it's not even a scratch" (Toughness Bonus ftw) and "ohmygodinstakill!". This in itself is something I actually find more worrying than the "merely average" minimum damage.
If it were up to me, I could see the Turbo Penetrator being changed to a flat +10, which not only increases the minimum damage but also lowers the maximum damage to 32, somewhat reducing the lulzy randomness.
It's a "hypervelocity heavy gravity round" - even a grazing shot should hurt. A lot.