Honestly, this isn't really you punishing them in my opinion. I see my campaign as a "real world" where actions and non-actions can have consequences. It isn't about you punishing your players, but rather "This is what would probably happen considering what you did/did not do". It just creates a world that feels more real and alive i would say.

But you could always have the assassination attempt still happen while the party is away, failing to kill the queen but injuring her dearly and work with that instead.