If it's a modal it won't hurt your SEO, we ran a number of promotional "Modal boxes" - (not pop-ups per se) and it didn't make a difference. Then again, the site is a popular brand and has more than a million visitors a day. So I wasn't expecting to fluctuate.
If you want to be fancy - don't show the modal to SE Crawlers. Here's one way of achieving this. Mind you I haven't read the article, so there might be better ones out there. But detecting bots isn't necessarily rocket science - especially if you are on a Web Application Framework like Rails or Django. CMS wise I am not necessarily the go-to guy.