Here are my answers to your questions:
"My main question that I want to ask you is do you think that Alex should have any custody over Isaak..."
Yes. Not letting the baby have time with his father is wrong.
"...if he can threaten me and sometimes threaten Sara?"
Domestic violence and even serious threats are a valid reason to restrict contact, but this must be proven.
"Another question is do you think that I'm doing the right thing to parent Isaak because his dad really doesn't care?"
I think you are right to support your fiance in her parenting, but I wouldn't assume the father doesn't care. Not showing interest "until recently" doesn't mean much in such a young child. You are pretty "recent" yourself.
"And could Alex really get 50% custody of Isaak like he says he can."
Yes. In fact, he can get more than 50%, but I don't think it is likely. Best to take a support role and hopefully the parents will cooperate.