Your tent's stress points should be reinforced well enough that they should not be damaged by staking them out tight. If you don't see any signs of fraying, stretching or warping at the stress points, then there probably isn't any reason to worry that you are staking things too tightly.
The main thing is that you want to keep the fly from sagging onto the tent body, taut enough to shed rain rather than pool it, and secure against the wind. Flapping in the wind is not good, both for the noise and because the alternation between slack and tight tugs at the fabric over and over, and is more likely to do damage than if it just stays tight.
This April we were camping in our brand new tarptent at the Bearpaw High Sierra Camp in Sequoia NP. Since it was out of season, all of the tent platforms were bare, and we thought it'd be fun to set up the tent on one of them. We did this, but it was an extremely tight fit and we ended up pulling one of the seams apart a little bit. And Tarptents are supposed to be some of the most durable tents around!
Moral of the story: There is such a thing as pulling your guylines too tight.
That said, it was a simple fix, and well worth the experience:
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