well her being married makes it more likely that Mary I will killer her or cut out of the line, philip is also more likely to try to play for his rights and the French might make war for Mary Queen of Scots rights, also the crown would likely pass right to her Son and over her
Disagree. First, on your last point, the crown would not pass over her. The English throne earlier may have had more wheely-dealing when there was a candidate of preference, but by this era the rules of inheritance were set and were the same as they are now. The rules of male-preference primogeniture say that the throne passes first to a monarch's eldest son, then his heirs, then to younger sons in order of age, and their heirs, then to his daughters. In the case where the King has no living sons or heirs from them, but only daughters, the daughters will succeed to the throne in age order, with their heirs. In Edward's case, as he died before marriage, the line of succession passes back up to his dad - to Henry VIII's children. Obviously it's a confusing case since both Elizabeth and Mary had been made illegitimate but religious politics had forced that hand and religious politics would decide which of the two of them would ascend Edward's throne, but the point is that a pregnant Elizabeth would ascend the throne before her son because she has preference for being his superior (as his mother).
Philip probably will play for his rights, but then he did in RL too. Note that when he married Mary he had to sign an Act of Parliament saying that he would make no claim to England - Parliament also refused to allow him to call himself King of England for the same reason. He never had any English title, except Prince Consort, which is a title which disappeared when Mary died. Of course, he tried to claim the throne anyway, but he was fantastically unpopular and had no chance except by raising an army. There's little reason to think he would do any different to what he did IRL. In fact, with Elizabeth's husband just dead he could just try harder to marry her again, and I laugh at the idea of him thinking he can dominate Elizabeth.
I also have my questions about whether Mary would kill Elizabeth off - it certainly wouldn't be a decision made lightly and was something which was only historically done a handful of times for a reason. In Mary's case she wouldn't even have a reason to execute her, at least the vast majority of cases like this were done to pretenders who had technically committed treason and thus could be imprisoned legitimately and executed with "just cause" even if it would have to be done in secret. On the other hand, of course Mary would try to cut her out of the succession, but then she herself had been cut out of the succession (as had Elizabeth so there was technically no reason to do it again when Elizabeth wasn't her heir anyway) and yet look how successful it was at stopping Mary taking the throne...