The way I deal with the issue differs from playthrough to playthrough.
I almost always use geo/grav science vessels in a single neat package, but they're around 14000 tons in magnetoplasma era, and when I lose one to NPR or Spoiler races I tend to get quite mad. It makes for a nice RP moment, but still. . . so I've come up with a way of exploring that's a little less risky.
First, I postpone the exploration of every system but the ones in direct proximity to Sol to at least Ion Drive era.
Then I design a jump-capable carrier. No armament, enough hangar space to hold 4 survey ships. Its main feature is an enormously powerful sensor array, both EM and thermal.
These survey ships have thermal reduction on their engines, they're rather slow-ish and they have an extremely low thermal emission. They have decent thermal sensors.
The exploration strategy I employ with those vessels is:
-Send the carrier through the jump point. Out of 250+ explored systems in the current playthrough I've never found a threat directly in range of a JP.
-Move the carrier in a position that will guarantee a nice escape route if needed, but more importantly enough EM/thermal coverage to pick up any colony or ship that might be present.
-In case of a 2. 00 colony cost world I suspect might be dangerous even if the sensor coverage says otherwise, I will approach it very carefully with just a single science vessel.
I know it's not revolutionary or perfect, but I've explored thousands of systems with these ships and I've never, ever lost a single ship. I'm not home right now, but I will share the designs another day if anyone's interested!