Thats stratologger looks very impressive. All that you need now is packet transmitter that will sent data from rs232.
Please browse the site:
Byonics - TinyTrak3 GPS Position Encoder so you will get rough idea how it works and looks.
Of course major problem is that in theory you are not allowed to use default APRS frequency (144mhz) and you need to find an solution using PMR446/FRS/GMRS frequencies. That is becasue you are not legally allowed to transmit on amateur radio band (144mhz) without a license.
But there is many ready to use solutions like that: **broken link removed** (please look at the link, as its in fact almost THE thing that you need!).
Or you could just get a basic license (look for "amterur radio license") and go with standard and popular aprs hardware.
By using omidirectional antenna mounted on the top you could solve your fears about damaging the antenna.
Please look at this image: **broken link removed**
This is typical 70cm antenna connected to previously mentioned device. So now you have idea how small it can be.
In matter of fact this antenna could be nothing more than just pice of wire. Or even better you could mount it like that:
https://www.hamtv.com/giffiles/rocketantcamdet2.jpg in the middle of the rocket.
One more thing: its perfectly possible to make good antennas for very low cost (its just pice of wire!). So dont worry about damaging them at landing
ps. 70cm band is not much affected by ionized particles so rocket engine will not have much negative impact on transmission quality.
pps. This is exactly what you need:
index rocket transmitter
index earth recivier
Altus Metrum GPS Payload
Its kinda expensive IMO but whole design is open so you can build it yourself (or someone else) from basic components.