How about some additional chest armor perks that help you withstand these effects. They could go something like:
Burn resistance- reduces the duration of burn
Poison resistance- reduces the duration of poison
Flash resistance- reduces the duration of blindness
(I added the flash resistance because I think it would be a nice choice to have as well.)
I think these ideas would be a great solution because it helps out the people who dislike damage over time (or blindness), while also making them think more strategically about the armor they wear. The best part is that Thorn, Firebolt grenades, and anything else that burns or poisons remain untouched.