Two borgs in proxmity does not "negate their downsides", even slightly.
Flash each borg, they're both disabled for a few seconds.
They don't move very fast unless they have VTEC, at which point they about make pace with a human. Stun 'em and outrun 'em.
EMPs are great and all, but thrall a roboticist/get robo access/emag and suddenly you can flash->pull cell and the borg's out of service. You can even pull the brain at that point if you want the borg gone.
Cut AI control wires. They have to stop and hack each door back individually. Bonus points if you cut the power to the door.
Teleport into the RD's office, self destruct->enable.
Flash-spam them and just beat the borg to death. Hit, hit, flash, hit, hit, flash.