Personally I'm not sure if the queen is actually dead. I mean, in the opening cutscene, we see that the queen's powers can extend far beyond mere ruling. Maybe she found a way to escape using her literal space magic? I dunno...
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As a general rule of thumb, if they don't show the character dying then the character isn't dead. Or at least they will come back. That ball of light that you see every now and then in the dreadnaught, the one that keeps running away but always leads you in the right direction. That is at the very least related to the queen in some way. Its definitely not a bad guy and the queen says she had someone or something hidden inside the dreadnaught.