But maybe you can add it as a “hidden” feature (at least to the premium version)? I’m pretty sure many users have some control over their server configuration and can increase the execution time or install new php libraries. You could i.e. use a filter or action to activate the pdf index ing and then only experienced users/devs who know what they do can use/activate the pdf feature and the others won’t bother you.
Btw SearchWP can also index pdf files without xpdf but the results may not be as accurate as with xpdf. I also found this project: http://www.pdfparser.org/ which may help you to index pdf files better/faster.