There is, for instance, a significant strand within islamist thought that democracy is incompatible with islam.

Uh, not terribly significant, no, not in terms of numbers or dominant schools of thought.  Most Muslims do in fact reject the Salafist school of thought on that, and on most other things.  In my experience, the people who think of Islam as incompatible with democracy tend not to be Muslims.

Quite how the muslim brotherhood square this one I don't know.

The Muslim Brotherhood says it is fully committed to democracy.  What we don't know is whether they mean it.

What we do know is this:  Despite being officially banned in Egypt (which raises significant barriers to electoral participation) and despite the fact that Egyptian elections are farcical at best, it has participated in every election since 1990.  (It boycotted in 1990 in protest against an unfair electoral system, but had been taking part in previous elections since the 1970s, when they renounced violence.)

Every election, there are waves of arrests of Brotherhood members; at the moment, there are more than 500 of them in detention because there's a municipal election in a less than six weeks.  Every election, the systemic barriers to their participation and success are raised still higher.  (In the Shura Council election last year, the repression and fraud were so complete that they didn't manage to win a single seat, despite having won 20 percent of the seats in the lower house of parliament a year earlier.)  Every election, they keep participating.

The Brotherhood is aware that its legitimacy among the people derives in part from its commitment to the democratic process, flawed as it is here.  It is a tremendously diverse organization, with leaders that are moderate and those who are less so.  The regime is pressuring the Brotherhood in an effort to marginalize the moderates, because they need the so-called West to be afraid of the Islamists.  They need the Brotherhood to be a scarecrow.

Genuine democracy might indeed bring groups such as these to power.  Genuine democracy might also quite possibly remove them from power.  The expectations for adherence to genuine democracy should not change depending on the results.  One looks rather absurdly hypocritical when one demands that an Islamist party act like perfect democrats, when one is not willing to expect the same of the so-called "secular" parties.

Something the so-called "West" has never seemed to learn is that the steadfast support of fundamentally corrupt, repressive and undemocratic regimes only strengthens the resolve and popularity of the Islamist alternatives.  If they really want the so-called "secularists" to triumph, they'd be better off backing the Islamists.

Would I want to live in a country run by the Muslim Brotherhood?  No, probably not, at least not if I didn't have a foreign passport that would allow me to leave whenever I wanted.  But if the democratic system were working properly here, I really do believe that they amount of super-conservatism that their most conservative leaders would be able to impose here would be limited -- limited by civil society, limited by popular lack of desire for such sweeping changes.  But nobody has ever encouraged the development or strengthening of such a system here, so yes, the "spectre" of "a Brotherhood government" feels somewhat more intimidating.

Again, this is why supporting institutions and the democratic system should be the goal, rather than supporting parties or individual leaders who are allegedly ideologically aligned to us....