Not necessarily; for example as of right now we really can't track single people still via infrared from orbit. Even single vehicles is tough, unless they're large vehicles like ships. Similarly at this point in time there exists natural insulation good enough to retain 100% or nearly so of heat generated. Go look at a polar bear in the infrared sometime. They show as ambient temperature except for the nose and eyes. And if they can do it...
STOP MAKING COMPARISONS TO USING IR ON EARTH. Earth is much, much hotter than space, and therefore it is much, much harder to see things. Load up an FS2 mission and try to track targets while staring directly into the center of the sun. With the HDRish smartshader on, or drive while another car's high beams are being reflected into your face. That is what using IR to track people on Earth is like.
Perhaps IR sensors are complex and fragile now, but this will probably not be the case in the future.
There are, perforce, objective realities that militate against; one of them is the cryo requirement, which there is simply no way around. You have to cool it. You have to give it as little insulation as possible so it doesn't retain heat or cooling it gets much more troublesome. This is basic physics at work. Armoring such a system is simply not practical. You also forget that while yes, it may be possible to build it tougher, weaponry in FS is ridiculously powerful to the point where modern tactical nukes are only decent ante.
Considering the kind of combat we see in FreeSpace, we could easily sacrifice range for durability. Also, creating a material capable of withstanding multi-gigaton direct hits is completely impossible, so magical handwaving materials are
already present in FreeSpace!
Even assuming all these things are possible you must then pick out this target from all the other faint infrared sources you'll detect out there. This is no mean task. There will be thousands of such sources, many of which will not be matchable to objects in visible light or existing planets/moons/asteroids, many of which will be transitory or new. A background or at least some grounding in astronomy would do you good. With an exposure time of each image of, say, an hour (down from the several it takes today), anything that has discernable motion in that time will be spread out and lost as it did not emit enough from the same spot to show up.
It's a wonder how radar operators manage to make out anything with massive radio sources blasting away from all over the world, then (the Earth produces more radio waves than an area of the Sun equivalent to Earth's surface area. That's a
lot of radio waves), or radar signals reflecting off the ground, clouds, etc. It's not that difficult to discern a moving target from non-moving space. Furthermore, you're thinking of a
telescope, while my idea is a more advanced version of a police thermal imaging camera. But wait, it gets even better! A ship like an Orion-class destroyer is not going to be a faint IR source. To move several billion (yes, billion with a B) tons of starship and power multi-gigaton beam cannons, you need an almost inconceivable amount of energy, This energy is going to result in a similarly incredible amount of heat and radiation in multiple spectra--IR, visible, UV, even X rays! Even in an hour, an Orion won't move very far in astronomical terms, and if the signal does spread out, you're going to get a very bright line along the Orion's course. If the heat of the crew compartment is a beacon, the energy released by its engines will be an enormous flaming arrow pointing down from the sky, visible on UV and X ray detectors as well as on infrared.
An Orion is not a faint signal. It is a huge signal. Woe be to any planet it enters the atmosphere of, considering the amount of energy put out by its drive engines alone.
You might as well make it a gigantic bomb then. You're not going to create that much IR unless you're dropping nuclear mines out the back of your fighter. Using thermal imaging on Earth is like standing on a floodlight, and we can still resolve people and animals. It's unlikely to fool a missile and it certainly won't fool the ship that launched said missile.
I was talking about missiles like the Harpoon, which we have no modern equivalent of. Aspect-seeking missiles lock on by the shape and possibly texture of the target ship's hull. Providing a completely dissimilar decoy will not fool a Harpoon or Trebuchet. Also, a modern aircraft's engine is like a firecracker compared to those of even FreeSpace fighters, which have been shown in command brief animations in FS1 to go from the surface to space in a matter of seconds! Such engines would likely be brighter than a nuclear explosion, and devastate anything that followed a FreeSpace fighter too closely. Try hiding
that with a chaff pod (you can't).
Who said you aren't dumping nuclear mines out of the back of your fighter? But let's be realistic. An unshielded nuclear reactor has a thermal signature to rival the Sun, which was one of the reasons that the ASAT program used infrared seekers for the proposed task of shooting down nuclear-powered Russian satellites. Dumping a short-term unshielded fusion reaction out the rear end of your fighter is entirely feasible and quite within the realm of possiblity.
FreeSpace ships already "dump an unshielded fusion reaction" out their engines, as evidenced by the description of gas miners collecting fuel for "fusion drives". They take plasma out of a fusion reactor's core and spew it out the back--a massive fountain of intensely radioactive plasma blasting out of your ship at obscene velocities. Face it: stealth in space is as much technobabble and hand-waving bull**** as doing loop-the-loops and banked turns in space, humanoid Vasudans, color-changing Subach blob cannon "xasers", and subspace.