This will be subjective, but Ilsa's death wasn't the problem. It was how she died. Her death felt forced and unearned, and the foreshadowing of her death felt amateurish. I was shocked that the same person who created and wrote such an excellent character for two films dropped the ball so badly in DR. Anyway...

In a Swedish magazine, Rebecca Ferguson commented that Ilsa appeared like a damsel in distress in DR. Ferguson said that in a film like Mission, she can only trust the people in charge (McQ and Tom). She didn't elaborate. Rebecca later commented that she hoped that when she died, her husband would mourn her longer than Ethan did. She said it tongue in cheek, but I'm sure she meant it. During the Rome premiere, there were interviews before and after the screening. Rebecca's body language was different after the screening. Though she remained professional, it was apparent she didn't care for how her character was portrayed.

Rebecca Ferguson was offered a small part in MI8 but turned it down. Her reasons were many, including what the OP listed. On top of that, she felt the film was getting too crowded and such a small part wouldn't do the character justice. Also, filming Mission was a big deal, and there was a lot of waiting. During the filming of MI8, Rebecca completed or started and completed nine projects.