Two options

A) Tell your Nin to get more HP (This sort of stuff is why we recommended 6.5k hp for our melee/bard whilst learning the fight).

B) Otherwise your suggestion is pretty close to how I handle that mechanic, I precast medica II as megaflare starts casting, then time a medica 1 to land in-between the megaflare and tower hits as you say, with practice it's pretty straightforward to consistently land it without the need for swiftcast.

http://www.hitbox.tv/video/348756

Note that normally I wouldn't swiftcast that Medica II, trying to get a stoneskin on the OT (3 rage stacks oops!) kind of forced me to mix it up a little