It's easy to get them to behave, threaten to mind control the crazy melee adept they have (assuming she doesn't use all her edge to avoid it)

On a more serious note (I can't believe I'm going to give advise that will cut my groups profits), you have several options.
Make the matrix security a little stronger.
Make them keep the money on a seperate node, or in a banking institution.
Have non-electronic funds like credit chips (although, that didn't help in this case)
Have the money split across a large number of accounts and overseas holdings, make the hacker chase after every credit they can find.
The other thing you can do, is have said group have a secret reserve, and they use it to hire a hacker/shadowrunner to get their money back.
That's what I can think of at the moment, I'll post if any more ideas come to mind.