I own a Sony Reader Touch, which is an competitor to the Kindle. It is around that size and quite happy to handle documents such as approach plates as pdfs (or manuals as MS Word files). It also lacks the keyboard (which I doubt you'd want), doesn't have any form of RF capability - which would make me much happier in a cockpit, and doesn't have any remote capability for Amazon (or anybody else) to modify or delete documents on it.
I have used it in flight for taking notes - it fits into an A5 kneeboard happily enough (or, just, into a suit inside jacket pocket), is easy to read in most light conditions, and (so far) very reliable. The ability to "write" onto printed documents and turn your handwritten notes on and off may well be useful in the air. PDFs do want to be A5ish or they're a pain, and opposite to conventional screens, the more light the better - so in bright sunlight it's superb, but at night it's fairly useless. I don't think that any of the current generation eBook readers have backlights (but then again, there's cockpit lighting and the backup torch).
So, I think that the OP's points are good ones, but personally I don't think that the Kindle is the eBook reader I'd look at first.
Both of course also have the huge advantage of taking loads of reading matter for those weeks away when you need to find something to do with your evenings that doesn't actually carry risk liver (or other physiological!) damage! My Sony (with a 2Gb SD card in the expansion slot) is currently carrying about 50 novels, a manual on test flying the size of a telephone directory, and about a dozen scientific papers - diagrams and all. It's nowhere near full. It charges on a USB socket, but only needs charging about once a week of substantial use.
The technology is definitely good! Details on the Sony are
here; I got mine for £220 a couple of months before Christmas from the WH Smiths website (a large UK chain of bookshops). And no, I don't have any shares in Sony, I'm just very impressed with it.
G