Not necessarily. Time travel in the 616 is a little tricky. More often than not, you don't really travel to your past. You travel to an alternate version. This multiple worlds theory allows the writers to freely muck with time travel stories without screwing up continuity. It's only on the rarest of occasions that you actually see time travel in Marvel change the present. Even so, you can argue that, in the case of AoA, Legion killed an alternate Xavier and what we witnessed was the result of that - with Bishop along for the ride.
I'm thinking that even if you kill Young Scott, nothing will come of it. You will only have succeeded in killing an alternate version. Clearly, OG Beast has no recollection of ever having met himself when he was a kid. That'd mean that Xavier either mind wiped him or it never happened in prime continuity. In the case of the latter, that'd validate the the Young 05's existence as alterna versions. The longer they stay here in the present, the more they'll deviate from their original selves. When you return them, you can wipe their minds, but you can't explain away how they've aged.
IMO, all Beast did was kidnap alternate versions, screwing up their timeline, just to make a point to OG Scott. A little Power Point presentation might've been simpler.

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