Imagine this...

[Beyond Batman]

Let's say you have three characters lined up perfectly. In order, you have Huntress (V) and Batman (E) in adjacent squares. Now your opponent has Brainiac 13 (R) within range and has line of sight to both Bats and Hunts. Now Brainiac would like to attack Huntress yet Batman is in the way. But technically Batman is in stealth so he can't be targeted. Can Huntress be attacked in this situcation?

[HeroComplex]

There's a contradiction in your situation. You say that Brainiac has line of fire to both figures, but then say that Batman is in the way of his LOF to Huntress. But since the question only comes up in the latter case, I'm guessing that's the situation.

No, he cannot attack Huntress. The LOF crosses a square which contains the base of another figure, and therefore the LOF is blocked. The fact that Batman has Stealth/Batman Ally doesn't enter into it.