This seems a deal-breaker for me to recommend the tool to my company. We want to try this plugin within team without affecting the JIRA performance of many other software projects, some of those projects being quite large.
I'm happy to inform you that in the newest version of issuegraph (2.1.0) there is a feature to disable the plugin for projects.
As it is still not possible to disable whole plugins for single projects (in fact this is an ongoing feature request at atlassian) issuegraph now skips rendering and displaying the graphs for disabled projects. However you will still see the issuegraph headline at the issue detail view just without any content.
Hope you can work with it.