The Windows publisher wasn't the same as the Linux one, for starters- Loki did the Linux version, Activision did everything else. Activision had nothing to do with the Linux rollout which was delayed 2-3 weeks because of a last minute logistics snag. If you're trying to send a message, though, wouldn't you try your level best to resist the impulse there? Buying the Windows version and "patching" it sent a message- it told iD, Activision, and others that nobody really wanted Linux titles (they didn't put their money where their mouths are...). As far as they know, Windows is what we wanted because that's what we BOUGHT. It's not a hard concept to grasp, when you stop to think about it.
Buy what you want to run against, if it is offered. The two weeks that it was not available didn't impact anyone that would have bought it for Linux because if it's going to be "dead" on the servers in that small a span of time, it wasn't worth having to begin with. We didn't buy the Linux version. We bought the Windows one. Doesn't matter how many downloads, etc. of the Linux binary sets have been made or how many Linux clients show up on the servers. What sold matters to the publisher and to a lesser extent the studio. In this case, what sold was WINDOWS. And Activision noticed that. So did iD. Obviously Loki didn't fail to notice it- it was one of the fatal turning points for the company.
Now, if it's offered by the same publisher, it's a bit of a differing story- and it probably ought to be offered at the same time or close thereafter. IF it's from the same publisher and not a gift to us like iD and Epic did with their stuff. Only some special bundle packs of Doom from MacMillan and Q3:A were ever actual official, published FOR Linux SKUs from either of those two publishers.
As for the bulk of the sales being in the first two weeks... That's the justification they use to put DRM crap on everything. It's NOT quite that way (If it were, why would retailers like WalMart stock some of the SKUs in question for MANY months? If it sold the bulk of it's sales in the first two weeks, then why keep it on the shelves when you could get something that WILL sell back on the shelves...)- it's a wives tale that people keep spouting from time to time.