The deaths in X-Men 3 didn't make it a bad film. It was the reason for the deaths and the way they were handled. Cyclops was killed after three minutes of screen time just because he wanted to work on Superman with Bryan Singer. All the other deaths fell flat because Brett Ratner can't film emotion. He wanted to kill characters for the simple sake of killing characters.
To be honest, I didn't mind the deaths in X3 - but many fans did. A lot of fans and viewers did not want to see Xavier, Cyclops and even Jean killed off, or Rogue and Mystique cured. No matter how it was done.
The film was clearly intended to be a 'last stand' - a final chapter in that series. However, all those deaths and curings were not necessary. While Rogue taking the cure would no doubt be the choice of most teenage girls in the real world, it went against the themes of the movie. Cyclops could have been recast had they really wanted the character, but they chose to use the death to push forward Phoenix's arc as a destructive force who had reached a point of no return.
Most people just didn't want their favourites to die or be cured, that was the main problem.
To say the characters should all be completely safe from death really handcuffs the filmmakers and makes the movie feel safe. If there's a good reason to kill a character, a powerful scene in which to do it, I'm all in. Matthew Vaughn is a better filmmaker and writer than Ratner will ever be, and if his story involves knocking off Banshee or whoever, go for broke, man.
I think that you have to be careful with killing off key characters. Especially in the wake of X3, but also because of taking away people's favourites or defying the source material.
I would not be entirely comfortable with Banshee or Havok being bumped off. In the comics they both leave the team at various points - Havok goes off with Polaris when the new X-Men (Storm, Colossus, Nightcrawler etc) arrive, and Banshee sticks around but leaves (for Muir Island to be with Moira MacTaggert) when he loses his sonic powers after overstraining them in a battle. I think following those ideas would be the best thing. Have Banshee lose his sonic powers (and his voice) while battling a sonic weapon.
In the case of Havok though, I think that his death might be one way of motivating younger brother Scott to step up as a leader. But I would still rather they follow the source material and not bump off any main characters that don't die in the comics.
I would, however, have no issue with Angel (Zoe Kravitz) and Riptide being killed off during a botched mission.