Vegetarians and Mezuzot
One option is simply using mezuzot and other ritual objects that involve animal products when they are deemed halachically necessary. I do not know of any mezuzah scrolls that can be confirmed as having come from humanely treated animals. Jewish Vegetarians of North America takes the following position:
The number of animals slaughtered for [ritual object] purposes is minute compared to the billions killed annually for food. The fact that there would still be some animal slaughter to meet Jewish ritual needs shouldn't stop us from doing all we can to end the horrible abuses of animals. Also, most problems related to flesh-centered diets -- poor human health, waste of food and other resources, and ecological threats -- would not occur if animals were slaughtered only to meet Jewish ritual needs. Our emphasis should be on doing a minimum amount of harm to other people, the environment, and animals. The fact that some animal products are required for sacred uses (a very small amount) should not prevent a person from becoming a vegetarian.
Another option is knowingly using non-kosher, vegan scrolls instead of animal parchment. It's not the same as using the real thing, but the argument could be made that it's better than doing nothing at all. The late Dr. Daniel Kliman (click here to read my obituary post) once noted in a VeggieJews e-mail, "You can get [mezuzah scrolls that aren't made from animal hides] in just about any Judaica shop or synogogue gift shop. You can usually get them for about $2. The problem is, they ain't Kosher." If you're looking for a DIY non-kosher approach, check out Rabbi Zalman Schachter-Shalomi's thoughts on making your own mezuzah scroll.
These issues can be hard to deal with when thought of as a battle between different parts of a person's identity or a conflict between religion and ethics. Nevertheless, it's important to confront them head-on and with integrity, as was discussed at Dr. Kliman's memorial service. It might be hard to reach a definitive conclusion, but that's OK. As Rabbi Steve Greenberg (the first openly gay Orthodox rabbi) has said about such conflicts, "Often, the holiest place to be in is the place of being stuck and not knowing what to do."