Instead, Obama supports the take over and defeat of other governments either friendly to us, or neutered by us, in favor of radical Islam regimes that are coming to power.
Let's remember, that Obama didn't support the protests in 2009 because he said, they were 'internal disputes' between different "factions" of the same Islamic Regime.
To some extent, Obama was correct. Especially, since the media & some "others" kept on portraying Karroubi & Moussavi as "leaders" of the Green Movement. Both of whom have a long track record of being part of the IRI. The latter has had more than a few 'black marks' on his record. And, neither one wanted to see the downfall of IRI. They just wanted to take over from Ahmadi-Nejad.
But, as you say, Obama could've used that opportunity to bring the end of the regime, in its entirety. He chose not to.
However, in Egypt, Tunisia, Libya, the emphasis was put on "democracy" and "human rights". So, the Obama type logic, which has not been unique to his administration, suggests that if the people choose an Islamic Regime by democratically voting for it, then that is perfectly acceptable.
All is all, I think there has been too much emphasis on "democracy" in the ME, N. Africa & generally the moslem world, and not enough on actually choosing the best regime to govern, not only domestically, but also in its foreign policy.
We can't continue to transpose western values & practices on others, particularly in the moslem world. Democracy is not a product, it is process that often is historically & culturally-specific. It is a process that, most likely, will take generations to introduce & embed in Iran & generally other Islamic nations.
Naturally, you've to start somewhere. So, firstly, any "radical Islamic" regime requires a radical change, politically & socially - when necessary, by force. Once that is accomplished, we can embark on introducing democracy. Ultimately, it is about "Cultural Change".