I chose to work for a place that judges me by what I produce, not by when I come in to the office. The beauty of being a software engineer in Silicon Valley (and I imagine this is the same in other technology hubs such as Seattle, Rte-128 and Austin) is that I get this choice. Here's a prediction: companies that micromanage in this fashion simply won't attract the required engineering talent. All else equal, engineers will choose a place that gives them more flexibility. The market seems to confirm this. Here's an interesting thread on hours engineers work at Facebook on Quora:
http://www.quora.com/Does-Facebook-have-fixed-working-hours
Note: I'm not opposed and frequently make use of "lower-case-A agile" i.e., unit testing, re-factoring, iterative development but they are just common-sense tools; much like editors, IDEs and programming languages they are frequently treated as objects of religious devotion, overlooking the fact they may be right for some (in some organizations, even most) projects, but inappropriate for others.
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Just don't do that then. In at 9, out at 5. No problem, life goes on.
So for instance, on more than one occasion I was forced to wake up and fix a chronic problem caused by another team at 3-4am,and would show up at 10:15 and miss he scrum.
Got chewed out for being 15 minutes late on only 5 hours sleep.
Worst company ever.