Since the reshuffles of 2012, many of the terminals have changed around and companies have moved. So be sure that you're going to the right place.
However, it sounds like you know the details, so assume it IS in Zona 1, which Wikitravel seems to agree with, you may consider this advice from Frommers:
Guatemala City is not very conducive to exploring by foot. The city is
spread out, and many of the major attractions are far from one
another. Plus street crime is a problem. It's relatively safe to walk
around zonas 1, 4, 9, 10, and 13 by day. However, with few exceptions,
you should never walk around Guatemala City at night.
Wikitravel seemed to agree with this, saying that many bus crimes happen on night-time bus rides, and that you should avoid travelling by bus at night.
Now if you've done bus travel before, you'll know this is all statistical and nothing is guaranteed - you may well be completely fine, and probably will be. It's a bus station, with staff around, other people watching, isn't in the middle of the night, and so on. However, opportunistic crime can happen at any time, so your best bet is to stay in a public, well-lit area, ideally near any security staff, to maximise your safety, if at all possible.