There is a lot of misinformation going around about this problem. This isn't an issue with Valve or with the developer, this is an issue with how chargebacks work.
1) Credit Card gets stolen
2) Thief uses card to buy a number of keys
3) CC Owner reports theft and starts to issue chargebacks(rightfully so)
4) CC Company takes money back from point of purchase(Steam or Developer depending on where they bought it from.)
5) This is the big part, CC Company takes an ADDITIONAL amount from point of purchase. This is money LOST from the seller, in this case Tynan.
6) It is the developer's job to disable Steam keys which often happens and is happening in this case. To be honest, I'm not sure if devs can deactivate keys directly or not but based on various indie developer reports I've read they do get deactivated somehow.
This is why buying from grey market sites such as G2A and CDKeys is WORSE than piracy. I know there are legitament sellers on those sites but you have no way of knowing if a key was bought from a chargeback or not. If it was, then not only did the developer lose money from the initial sale, they lose money from chargeback fees as well. I believe it was the Factorio devs that straight out said they would rather you pirate than buy from these grey market sites. Not because all sellers are bad, but there are enough bad sellers that it encourages this type of fraud to continue happening.
Either way you look at it, I think that it mainly boils down to CC Chargeback fees. It can be argued that there shouldn't be these fees from the CC company, but it can also be argued that it is up to the seller to prevent fraud like this. I don't personally know enough about selling from a shop online to know which side is more right but either way as it stands at the moment, the indie devs are getting hurt the most.
I believe Factorio got around this by requiring users to link their Steam accounts directly to their Factorio account and assigns the CD Key that way, like Humble Bundle used to do it(they might still do it that way, not sure). This will probably be the way Tynan goes as well if he decides to sell Steam keys through his site again.
Just keep in mind when buying this game, it has always been $30 for the cheapest version. If you see it selling for any less it is most likely a stolen key unless they are just buying keys and selling it for less out of the goodness of their heart.
Here is a link to the Facotrio post where they address this directly about midway down: https://www.factorio.com/blog/post/fff-145