Likewise; I wouldn't use any clip-on tuner on a guitar whose finish I cared about. Here are three options I use that I think are better:
1. A TC Electronics PolyTune pedal; absolutely the best such device available IMHO (and that of many others). Biggest downside: it needs to be in a signal chain, or for everyone else to be quiet.
2. The TC Electronics PolyTune App on my iPhone (I believe it's also available for Android phones as well). A great app; works essentially as well as the pedal, but can't easily be in your signal chain, so it does need quiet.
3. An old-fashioned tuning fork (solid metal, shaped sorta like a very elongated "Y", sounds one note, usually "A"). Tap it against a piece of wood other than your guitar and touch the single end against your bridge, beside the string pegs (where there's no finish). You'll get a beautiful, resonant "A"; tune the 7th fret harmonic of your D string to this. Now use your ears to tune the other strings.
In all seriousness, I use all of these, and #3 is my favorite. The more you use your ears with intention, the better they get, and you'll be able to hear very quickly when a string is going a bit out of tune and make pretty decent corrections on the fly. Conversely, the less you use your ears, the less they'll be able to help you. With reasonably good ears, you can even use method #3 when there's a fair bit of ambient noise around.