This is why I don't understand why fish is touted as a good source of Omega 3 fatty acids. If the fatty acid bonds are that easy to break with even low heat, people who eat cooked fish aren't getting any, and people who eat raw fish are getting more than they bargain for, in terms of unwanted passengers.
I'm not sure baking with flaxseed is dangerous though. You just won't get any Omega 3. If that fatty acids do turn from cis to trans, I don't think there's enough of them in a typical quantity of flaxseed used in a recipe to cause great harm.