So who told Brandon Stark that Lyanna was getting raped?

[Sasha Steelsong]

IMHO, there could have been multiple issues. If Elia nearly died in childbirth, I think it is very probable that she bled a lot, which in turn indicates being badly torn in the process (especially if Aegon was badly positioned). I doubt that maesters are able to perform plastic surgery of intimate parts, therefore there would be bad scarring, which would cause problems in subsequent births (scarred tissue is not as flexible as it needs to be) and possibly hamper sexual life, as well.

Concerning the trial: it seems that Aerys confused his terminology and switched trial by combat for trial by ordeal: I'm afraid, however, that even in this case he went a wee bit too far: http://en.wikipedia....#Ordeal_of_fire I can't recall if something like this has ever been used in Westeros, but I'm wondering: what exactly will Margaery's trial include?

I think Margaery's trial is to be one by the faith not by ordeal. While we haven't seen a trial by the faith yet, I'm guessing it will resemble Tyrion's trial until he opted for Trial by Combat.