Upvote:3
Officially, your wife has the right to be in any Schengen zone country as long as she is travelling and residing with you.
The gradual phasing-out of internal borders under the Schengen agreements was followed by the adoption of Directive 2004/38/EC on the right of EU citizens and their family members to move and reside freely within the EU http://www.europarl.europa.eu/atyourservice/en/displayFtu.html?ftuId=FTU_2.1.3.html
The eligibility requirements for the UK EEA Family Permit Visa do not mention current residence or visa status, so there is no reason why it should be an issue: https://www.gov.uk/family-permit/eligibility
However it is possible that your wife will have issues if you attempt to re-enter Portugal after your time in the UK. She will not have the right to travel alone and I have heard anecdotes of non-EU spouses without visas being denied at the border even though they are not officially required to have a visa. For this reason, it is probably a good idea to obtain a visa before re-entering Portugal. She should also be eligible for Portuguese citizenship, which would give her the same freedom of movement that you have.