Belgium already paid for it, in the form of the tax aid they gave the companies. It just turns out that it was illegal and said tax breaks, which Belgium already paid for, need to be returned.
I think we must clarify things and what "it" is
(1) Giving tax break is what Belgium wanted to do. Belgium offered aid, companies took it.
(2) The fact that said tax breaks (or aid) were illegal is the violation of the law that someone is supposed to pay for.
Belgium paid for (1), of course, that was it's intention. But it does _not_ pay for (2): it actually gets it's money back because of (2), if I understand correctly. Or this money goes back directly to EU, this is not important; anyway, Belgium is not losing money because of (2), companies are.
So, companies are paying for performing action that was completely legal in the law of the country they were operating in. Companies are paying for Belgium lawmaker's mistake.
If a region (say a state or a county in a state or a town in a county in a state) helps a company out and that turns out to be wrong, passing legislation it wasn't allowed to, why would you expect the company to also get off the hook? That would seem to provide an even greater incentive to perform corruption because once it's done, as the company you're immune from the consequences.
Especially big multi-nationals with lots of lawyers who knew the possibility that this exact thing would happen. They went in to this deal knowing full well the EU might turn around and say the deal violated the company aid treaties.
Get of the hook — for what?
You automatically assume corruption, I can see why. But still, (1) getting tax breaks or government help and (2) using illegal methods to get said tax breaks and government help are two different things. If you want to punish someone for getting government help, then you're using correlation of 1 and 2, but correlation does not always imply causation. And more importantly, in case of law people generally try to determine that someone _certainly_ did something wrong instead of relying on the notion that he did it with high probability.
So, if you can prove that the company engineered it through illegal means — feel free to do that. But don't forget that there are quite a lot of completely legal and ethically clean methods in lobbying. Quite often, all that company has to do to influence policy is to meet with the official and present their reasonable point of view on the issue, without any gifts, bribes or campaign contributions.