As I understand it the issue is she doesn't want to use maiden+married name, just married name so a deed poll wouldn't really solve this as the issue lies on the Portuguese side of things.
According to the HMPO's Knowledge Base, it
is possible to change your name after marriage in Portugal.
https://www.gov.uk/government/publicati ... se-profile but to be fair, I'm not sure if you can change it post factum or only when registering the marriage (for example in Poland you only have one shot at it when registering your marriage and it's nearly impossible to change it afterwards).
If you can't change your name on your Portuguese passport then I believe you won't be able to have only your married name on the naturalisation certificate as the one on your passport is indeed your legal name. Is there any particular reason you'd like to avoid it, other than your personal preference for your married name?
There might be some leeway with your British passport after you've naturalised using
administrative fairness test but it's a bit of a long shot and you'd end up with an observation listing your Portuguese legal name.