Well, since my bid time passed I guess I have an answer now, here is what happens:
Even though the guild who currently holds the maximum bid doesn't exist anymore, if someone else wants to buy that Guild House, then that person will have to outbid the non-existent guild.
This means I can Bid 100kk in a guild house, disband my guild and if someone else wants to buy it, he/she will have to pay over 100kk, as if there was nothing happening with the guild. In my opinion this leaves some room for abusing, but I guess that's a minor issue...
On a side note:
I'm not sure what happens to the bidder money, in case he wins the bid without a guild.
I'm not sure if the money gets deducted and he immediately loses the GH or if no money is deducted at all, would have to test it...