You shouldn't have any problem filing jointly (even though you have different residency status). Also, as you each have to qualify for the FEIE individually, it will not matter if you are the only one who qualifies (both spouses do not need to qualify in order to claim the exclusion).
With regards to the penalty, although I am not sure how it would work in the UK, I know in the US you should not face any significant marriage penalty. Given your incomes, the odds of you owing anything to the US are slim to none. As such, the exact tax rate you will face (25% vs 28%) matters less. If anything, the exemptions for married couples are higher, so you may even do better filing jointly than before when you were single.
I hope this helps!!