I had the predecessor game, F-19 Stealth Fighter. It came out before the F-117 was officially revealed. Those "assassination" style missions were always my favorite for the reason you cite. You had to sneak in and take out the target, but once you did you got lit up and had to evade the now very angry air defenses.
I'll never forget manually flying at 150 feet at 150kts for hours, using the keyboard only, trying to evade all the radars along the way, sneaking up just to the outer edge of your missile's range to the target, popping open the bay door, launching, slamming the bay door back shut and turning hard around, throttle to the firewall to get as far away from the scene of the attack as possible (still at 150 feet off the ground if you could manage it), then trying to sneak back out a different way than the way you came to evade all the aircraft the sim sent up looking for you.
Then you get back and have to land perfectly or else you just die and have to start your character all over again as a 2lt. You could, of course, hit ctrl-alt-del and reboot the machine so your character wouldn't die, because it didn't save anything until the very end of the mission.
I'll also never forget how amazingly better the game was when I got a color monitor and could see that the game had colors -- I couldn't see half the controls in black and white.
It was a surprisingly hard game, actually.
BTW, both f19 and f117 are available on steam. I still pull them up and fly them occasionally just for nostalgia.