Portugal will be fine. Promise to marry his potential eldest son to a Portuguese Infanta and they get another chance at producing an Anglo-Portuguese heir to England. All he has to do is wait a few months in between the death of Catherine and the marriage to Frances. One interesting thing that could come from their relationship is later disdain. Charles held on to affection for her after she was disfigured in 1669 due to smallpox, but that may have been more pity for a formally beautiful but dim girl. After all:
So maybe, married to her rather than simply having pined over her, the King of England might come to be less infatuated with her, although that depends on who writes their story. She had no children I could find OTL, but that may just have been issues with the Duke of Richmond and Lennox. So let's say she's healthy and can produce children. With a marriage date around 1663/1664, she'd be about 17 when they'd start sexual relations. Let's say it takes a year or two to get that all running, so their first child is born around 1666/1667. Let's have a boy, just to make it fun.
I'd say she'd be able to have between 3 to 7 children overall. Her sister had six, her parents had two that I can find. So let's say 4 surviving children, 2 boys and 2 girls. Naming wise will be standard Stuart naming conventions: Charles, Robert, Henry, James, Sophia, Catherine, Anne, Elizabeth ect. Charles was somewhat conservative, so let's have Charles Stuart, the Prince of Wales, his brother the Duke of Clarence, Robert Stuart, and the Princesses Sophia and Elizabeth Stuart. These children can come between 1667 and 1677, allowing 2/3 years between each birth, which should make sure the Queen is allowed to be pretty healthy.