To start with, it's governed by a board of political appointees from both parties who fight with each other regularly and don't have a huge amount of shared agenda. They're typically going to have much more loyalty to their party than the SEC. Beyond that, the actual staffers don't "own stock" in the SEC. These things add up to something much less "cohesive" (for lack of a better word) than the effect you get when you put a dozen people who have 80%+ of their net worth in the same company in a room together.

Regarding your first point, about people -- yeah. But none of them has a particularly strong incentive to protect the SEC as opposed to themselves -- the SEC isn't a cohesive group in the sense of ideology or in the sense of a corporation. And even if they were, the porn story isn't worth launching a risky investigation over. Like I said, the Obama administration has a definite interest in pushing cases being filed in this particular 3-week window -- the SEC as an institution? Meh.

You'd be surprised how many government agencies and employees just plain don't have the hard-edged desire for nefarious political influence. Office politics, sure, that's their livelihood. Advocating their superiors to do things "the right way" as they see it? Sure, who wouldn't. But political influence to the tune of playing the media? They'd be in a political role if that was really what drove them.

Suppose the Porn/Stanford stories break. These are both big media-genic scandals.

Now the public widely perceives the SEC as incompetent/corrupt/perverts. Congresscritters declare that "something must be done", so they fire a few people, maybe do a reorg. Oh, and assorted SEC higher ups become known as "that guy who didn't catch stanford" or "that guy who didn't notice all the perverts in his office."

This gives all sorts of SEC officials a perfect motivation for drawing attention elsewhere.

As for launching a "risky" investigation, what's the risk? The case fails, and the public thinks the noble SEC was beaten by the evil vampire squid? The worst case I see from this is that congress decides the SEC needs more money/power. Oh noes!