The following workaround seems to be giving me some success:

If you get the "unexpected magic characters" error, make sure you have a non-hardware wallet window open in Electrum (create a dummy wallet for this purpose if you don't already have one) and then close your hardware wallet window (or all your hardware wallet windows if you have multiple open - although IME having multiple HW wallets open in Electrum tends not to work well).  Then re-open the offending hardware wallet using Electrum's  "Open" menu.  This seems to work for me quite well (on OS X).  YMMV...

(EDITED because the above seems to work better than my first suggestion.  For the record, my previous suggestion was: "It seems to be that the "unexpected magic characters" message is, at least sometimes, not fatal.  Try doing something that requires authentication with the Trezor (such as signing a message) and Electrum might recover....")