With Bloodfort, isn't it Shinji who forces Rider to activate it in Fate and UBW? As for HF, she felt a genuine threat to Sakura's life from Archer and Rin, such that it'd better to put Sakura into a coma than to let her die. Lesser of two evils sort of thing.
However, if she had other means of protecting Sakura that didn't involve risking Sakura, I'm sure she'd have taken them. But I see that whole mess as something similar to Caster in that even if she wanted to do something in a better way, her nature/abilities don't allow for that to happen.