What ways are there to defend against infiltrator stealth?

Jammers. Whether it's a Raider with a Jammer Pack or a Sentinel with a Drop Jammer, Jammers make stealthed enemies visible when they get into range.

Generally, you would just send a player with a Jammer pack to take care of it because, since an Infiltrator is a light class, they are very weak indoors when visible. If you are in a situation where the same Infiltrator keeps going after a particular objective (attacking the flag stand or the generator), then ask a Sentinel to drop one of their Drop Jammers nearby. Whenever an Infiltrator comes within range of a Jammer, they will both be partially visible and have a red marker over their head as though they weren't in stealth at all.

As a prevention tactic, you can use Motion Sensors coupled with Light Turrets in tight entrances / corridors. But, this is only effective if the Infiltrator is in a rush and doesn't look before he leaps.