I'm unsure of whether lein install
can be run without generating a pom.xml.
The reason it generates a pom is that leiningen uses maven to grab all the dependencies. In fact, maven is able to get dependencies from clojars and leiningen uses it for the clojure dependencies as well as the java ones. Maven requires a pom.xml to specify repository locations and other configuration necessary to run javac (or any other build commands) in addition to a groupId and artifactId to deploy your library to a (potentially local) repository
Another possible workaround to your issue is to use changelists (specifically, if using tortoiseSVN, I'd use the ignore-on-commit changelist) to ignore your pom.xml in most situations commitwise. I believe this stackoverflow answer may assist you with how to do that in git.