Rhys Williams, the European 400 metres hurdles champion, and 800m runner Gareth Warburton were both forced out of the Games in Glasgow after being provisionally suspended for alleged doping offences.
Both men have protested their innocence, claiming they never knowingly doped, and Greene, a vocal campaigner against drugs in sport, is sure both are telling the truth, but admits they will still have to accept a punishment.
"When Gaz (Warburton) found out he texted me and I was really upset about it, because I know Gaz and lived with him for a few years. He's not that kind of guy," Greene, the former world 400m hurdles champion, said.
"Hopefully they can get to the bottom of things and find things out, because I do believe that they are not deliberate cheaters. They have probably just been careless or been misled slightly. That will come out eventually I'm sure.
"Even though me and Rhys don't really get on, I know he's not the sort of person to cheat. I don't think anybody in the Welsh or British team honestly believes they have gone out of their way to try and dope to get an advantage.
"It's just unfortunate, but as professional athletes we've got to learn not to take anything that isn't batch-tested. That's the way it is. Hopefully other people will learn from it.
"The running joke with Gaz when I lived with him was he lived off raisins and couscous because he couldn't afford anything else, so I don't think he's organising a drugs ring down in Cardiff.
"Hopefully they can come back from this as stronger athletes and continue their careers, because they are past 30 now, so I do feel sorry for them in that regard."
Warburton and Williams have both used Mountain Fuel supplements. The company launched an investigation to determine whether the product may have had a part in their failed tests, but its owner said last week he was confident it could not have been a factor.
Welsh Athletics admitted they were "obviously concerned" by two suspected anti-doping violations in such a short space of time and promised to conduct an internal review.
Greene added: "It's difficult because the standard line is 'don't take any supplements'. But there are plenty of supplements you take that are fine. Some things are batch-tested and some things aren't.
"I've not known anyone who has been in their situation before so it was a big shock for me and a big shock to everyone else in British athletics as well.
"There's bound to be a punishment because you can't get away with having whatever in your system. But hopefully they will look at the situation. They've already been punished quite severely in terms of missing the Commonwealths - they will be too old at the next one to be in any good shape.
"They had ambitions to be at the Europeans (in Zurich next month) as well so that's two major championships they are going to miss. Whatever ban they are going to get will probably go into next season as well, so they will get punished for it."