You're pretty much correct there. A hit to the hand is a combat ender, and there isn't a lot you can do about that. However, there are a few things that you can do to help mitigate this, to some degree. One thing to remember, though, is that GURPS combat can pretty easily become a game of rocket tag. At higher point totals, most builds have one or two ways of killing an opponent in a single hit. The 'attack the hand' trick is just one way of doing that at a lower point total.
It was pretty much ubiquitous for armoured soldiers to wear gauntlets in the time when melee combat was effective. Heavy Gauntlets are listed in the standard armour tables on Basic 284, and give DR 4 to the hand. Depending on your tech and magic level, you may be able to make better, high-tech or magical hand guards for enemies that know how often your player pulls this trick.
Do a google search for "basket hilt", and check out the images page. Basically, the basket hilt is a piece of metal that wrapped around the hilt of a sword, and helped prevent your hand from getting stabbed. I can't find any official rules for basket hilts, but it would be reasonable to add an extra -2 penalty to hitting a hand so equipped, like how a shield gives an extra -4 penalty.
There are quite a few environmental penalties that can be applied in a fight that can further aid someone attempting to prevent their hand from getting injured. A table with these penalties starts on Basic 547. Some good ones that are relevant for many combats are Shock (-1 to hit for each point of damage taken last round), Close Combat (-2 if the defender is within Close Combat range of the attacker), or Bad Footing (-2 to attacks at GM's discretion). The defender can also use some situational bonuses to increase their Defense roll, like the Retreat action (+3 to Dodge, but you have to move backwards), using a shield (+DB of shield), or All-Out Defense (+2 to one Defense for 1 round). It might be tactically intelligent to have one melee combatant in the front rank, focusing on defense, while the combatant in the rear uses a reach weapon and focuses on attacking.
An enemy with a crippled hand is still dangerous
Depending on how motivated the enemies are to kill the players, they can still be somewhat effective with only one hand. The penalty for using your off-hand is the same as the penalty for striking the hand hit location, so the enemies have the same chance to hit the player's torso as the player does to hit the enemy's hand.
If mechanical discouragement isn't working well enough, then maybe roleplaying discouragement will work better. Give the player a reason to not want to cripple your opponents. For example, maybe there's an order of knights who give cool perks to their members, but joining means taking oaths to fight opponents honorably, and not try to cripple them.
Talk to your players
If none of that will work, then you may want to just talk to your players about it. Maybe point out that if they keep swinging to cripple their opponents, then maybe their opponents will do the same. After the melee fighter players get their hands chopped off a few times, they might want to make a gentleman's agreement to not purposely attempt to cripple opponents. Then again, that might be totally cool with them.
Maybe it's not really a problem?
GURPS is intentionally super harsh when it comes to melee combat. It's entirely possible to be killed in one round if your opponent rolls well, and it's easy to cripple someone. One thing that you may want to consider is if that's a problem with the game that you're running or not. Maybe it's a good thing that your players don't immediately kill every enemy that they see, and instead leave them alive to deal with after the fight. Not only that, but unless the enemies are super unlucky or the players are doing 8 damage in a single hit, the defeated enemies will be able to regain use of their hand after a few months.