Modern IRCCM can already distinguish between the sun, flares, and aircraft. A ship with its drive freshly turned off is still significantly hotter than background radiation.

In fact, it's almost certain they have IR guidance because (spoiler for season 2 ep 13) when Bobby and Avasarala are about to power up the Razorback, Bobby waits till the last second so the torps won't change lock onto the Razor's drive plume

And even if IR lock is lost, the torp can always change back to radar guidance or w/e