Every time I've asked this question the immigration authorities have said you can request for a residence card or an extension of stay (if possible in that particular country). I honestly don't know if the 90/180 days is a placeholder for Non-EU family members because of the uniform format (looks like a regular tourist visa) or what the deal is.
Last time I entered Portugal, the border agent was specific about the fact that I had about "35 days left". I wasn't visiting for more than 15 days in any case, but perhaps he is not aware of free movement rights. Furthermore, Portugal even lets you extend your stay all the way up to 9 months so I'm not sure what he was on about but I suppose he was just being nice to let me know of the trigger date for a potential visa violation.
The 90 day registration requirement still stands though and although for EU nationals no one comes running after you, it's harder if you're non-EU.
On another note, I fly in and out of Schengen a LOT and I've never had an airline actually COUNTING the days I've spent inside (they would need to locate all the stamps, calculate days, etc.). They just look at the visa, validity, and done.
My gut feeling says that due to derived free movement rights, this should be fine. I remember reading somewhere that Non-EU direct family members are pretty much immune to visa restrictions because the operative word is
right. At the most I believe she can be fined the same amount as you would be fined for not registering your presence within 90 days. Apparently, that's the most that can happen. I read this over a year or two ago so take it with a grain of salt but perhaps the Directive or another handbook has info on how this stuff is to be administrated.
You might also have trouble when trying to get another entry visa issued once this one is not valid any longer. Consulates can be sticky about this kind of stuff unfortunately, even though it's a right. Things are getting better I think but who knows..