For my part, I was more worried about not being able to execute 3rd party modules that aren't supported on App Engine ... but even that apprehension disappeared with today's announcement of managed VMs.
App Engine is a no brainer for me now. The amount I save on not needing an ops team for a long long time overcomes any slight misgivings that Google might abolish App Engine in a few years. I don't think App Engine is going anywhere, BTW. You look at the number of languages they are adding, the number of people they are hiring ... to compare that to Google Reader is a bit ridiculous.