Kerachole should be your first line of defense given it's your mitigation tool with the shortest CD at 30s. The regen on it's surprisingly strong too.

Most dungeon bosses don't hit hard enough to really force you to use the longer cooldowns that much, while it's usually the trash pulls that tend to get spicy, so don't hesitate to use them if you feel the need to. I've had a fair share of tanks that's made me use Temperance with WHM or Seraph with SCH, while many of AST's main healing tools are all aoe too, so it's not a mindset limited to SGE either.

Also Tower of Zot has some especially nasty pulls for some reason and it's fairly common to have to fall back to GCD heals for the last 2-3 wall-to-walls, if that's what got you worried.