The Founders strengths are genetic engineering and the ability to maintain individuality inside of a collective. I think both of these have been shown to absolutely crush the Borg and the Founders would see the Borg as a fitting solution to the solids.

The issue is then you have poked God Emperor Sisko of the sacred temple. A being with unending rage against the borg, a willingness to commit war crimes, and the ability to exist outside of time. Sisko is the only captain who faced a power scaling issue of his own power being too high as he was literally born with plot armor.