Well, she was at a disadvantage against pretty much every opponent but Spock's stolen shuttle. The Klingons she couldn't make a dent in. The Red Sphere was just about to blow and still the guns of the Discovery couldn't have hurt it. The Ba'ul coast guard was going to make short work of her. Section 31 evaded, chased and outgunned her as it pleased.
Being able to run from every opponent was a big factor in daring to engage these enemies in the first place. Perhaps the same factor would sufficiently protect the heroes in the future? Unless, of course, future baddies can also teleport at will.
Why the future would be more advanced than the present is a bit of a mystery, though. Humanlike intelligence is about four billion years old in the Trek Milky Way. It has diversified since, so there ought to be intelligences at every level from "Look rock go bang bang!" to "Why bother traveling at infinite speed when we know everything about everything everywhere anyway?". Why would the heroes suddenly interact with a more advanced subset of that just because they move ahead a thousand years or so? (But perhaps they don't, and the local space is actually less advanced technologically than the Feds of the 2250s were?)