No. It won't ruin your chance to work for that university in the future.
They may not hire you right away next week or next month for this same position. But, they may consider other positions for you in about 1 year or more provided that you do not act unprofessionally in any way when you reject their offer.
As long as you don't say anything negative about their university or about the position or about the red flags when you reject the offer, they will still likely accept your application in the future.
People reject job offers all the time when they have better offers elsewhere from other employers.
If you give them a simple, general, and positive rejection reason, then you can reapply for the jobs at that university in the future. For example, you can simply say:
"I've got an offer from my employer that better fits my career goals at this point. So, I decide to take that offer. Thank you very much for your considerations. Best Regards."
PS: My answer assumes that you do not work as a professor, and only work in other positions such as software programmer, administrator, librarian, secretary, etc...