with Arduino, you are limited to Arduino, obviously.
I'm not sure what this means. You can use the Atmega328 chip, outside an Arduino. It can be programmed easily enough using various methods, one of which is to use the Arduino IDE. Or, you can compile at the "command line" level using avr-gcc and "make".
I presume you won't actually fling an Arduino development board into the stratosphere, there would be a few reasons not to, including weight and power consumption.
I do want to be able to use an SD card, because the final result will be prettier, but it looks rather complicated.
The SDfat library makes writing files to an SD card pretty trivial. Something like this:
SdFile myFile;
if (myFile.open ("foo.txt", O_WRITE | O_CREAT | O_TRUNC))
{
// if opened OK
myFile.println ("some_data");
myFile.close ();
}
I wouldn't call that complicated.