Bigger rockets have been launched in the past (notably Saturn V), and in the days when HF communications were more important commercially, there were no problems reported with the ionosphere recorded. If there had been, I am sure the FCC would have picked this as having been noted by members of the ARRL. Surely there would have been plenty of reports of the effects of launching through the various layers, indeed various governments (including the UK) have carried out experiments and regular measurements of the ionosphere.
The frequencies used by GPS are c 1.5GHz - these pass straight through largely unscathed. There may be some odd rotation effects for instance very occasionally, but unless you're trying to thread a needle from space, largely insignificant.
Not so much punching a hole, more just a minor ripple.