Thank you very much for your input, it finally works. I succeeded in crosscompiling the frontend and running it on the ArduinoYun. The 64 MB RAM is more than
enough to run the mserver and a frontend and connect to a remote midas server over ethernet or wifi. 

Yust for reference if someone tries something similar: to directly access the serial interface between the Linux running processor and the Atmel processor it
is required to comment out a line in /etc/inittab: #ttyATH0::askfirst:/bin/ash --login
 this line starts a shell on the serial connection, by preventing this it is possible to run more or less unmodified code (serial interface needs to be
Serial1) on the Atmel side and use the linux processor as slow control pc.

Thanks again for your help!