I'm not in certification but....
I would hazard a guess 390 is a "service" ceiling rather than an "absolute" ceiling.
Isn't the max "service" alt defined by an altitude at which ROC reaches a certain nominal value? (Out of interest, there must be a weight associated with this limitation although I'm not sure what it is?)
What was your ROC in complying with the RA?
If the answer to the second question is a value in excess of the answer to the first question, the a/c (IMHO) wasn't actually performance restricted at that level.
The limitation to my mind is somewhat artificial although obviously if its an SOP one should comply with it.
Oddly enough, I was thinking about this very matter yesterday, because climbing yesterday at a reasonably light weight to 370 (our max alt), my recollection of the ROC at this level lead me to think the a/c was probably capable of climbing higher. Certainly the high to low speed buffet margin was >15kts.
I agree with Intruder's and Earnest's sentiments tho'. Sounds like a fairly valid reason for the excursion in question.