I don't know if this might be of any help.
When I was pg with DD2 I developed an ear infection (not sure which form, sorry). I reacted badly to Eurythrimycin and Codeine (both innacurate spellings I should imagine) so had to stop after the first dose of each.
I took echinacea and used lavender essential oil in my ear and it cleared up within a couple of days of regular use, I also found the lavender very soothing. It might be worth speaking with an aromatherapist if you consider using these types of treatments.
Tea tree and lavender oils have been shown to be successful in combatting MSR (though I have to say, no more effective than 'conventional' treatments AFAIK) and I do believe they have a place in aiding treatment of infections, at least, they worked for me.
I really hope things improve for your DD, it must be incredibly upsetting.