Yeah, this bothered me. I think there might be something in the dialog at the very end that might get to this, and why Discovery still had to go - that maybe the threat wasn't as expunged as it seemed in the moment. But that they didn't even pause after it was known Leyland/Control was 'neutralised' was a big wtf moment for me, given that the undefeatability of Control was the whole crook on which the jump to the future hung.
I think we just have to write this off though.
I think something they will have to address, though, is the problem mentioned above in the thread about why Burnham was able to jump around multiple times, when the time crystal was supposed to be only good for one jump. Again this was a crucial point - the whole reason it was a one way ticket to the future.
If it's ambiguous, as it is now, about whether the suit can still jump around in time, they need to explain what happened there next season. It raises too many questions. There are many ways to do it, but they have to offer something - like maybe jumping actually recharges the crystal in a self-fuelling kind of way, and they didn't know this? Possibly it's how Georgiou gets back to the Pike era, if that's when the section 31 show is operating in.