It's always a hazard. All reconstructions have to be taken with a grain of salt.
"Slant rhymes" like this have been used throughout history. Shakespeare is known to have used them in some places: some of his rhymes aren't consistent through his works.
It does help that sound change isn't arbitrary. When one sound changes, other sounds change as well. An entire category of consonants may lose or gain voicing, or shift in point of articulation. When one vowel changes to another, a lot of words can become homonyms, so usually every single vowel changes at once. These are called Chain Shifts:
https://en.wikipedia.org/wiki/Chain_shift
So a single instance of a rhyme is a weak piece of evidence, but when you take into account all of the texts at the time -- and the texts from surrounding times, both before and after -- you can make a good hypothesis. That hypothesis can then be tested against future discoveries, and modify as appropriate.
That's why all Proto Indo European reconstructions are marked with an * to say "We've never actually heard this word so we don't know if anybody ever said it". They're aware that all hypotheses are tentative. But that's how progress is made.