Deploy Javascript files to a Puck from native code

I've been using building an android app to communicate with my puck over UART and that has been going quite well.
However, it is too slow and unreliable for sending large scripts.
Due to the limitations of writing to Bluetooth characteristics, I have to write them in this way (excuse the pseudo-code):

10:
GetNextChunkToWrite();
SetTXCharacteristicToChunk();
WriteTXCharacteristic();
WaitForCharacteristicToBeWritten();
Goto 10;

The problems with this are:

1. It often takes longer to send (especially compared to the Espruino WebIDE).
   
2. If the puck is in the middle of outputting something, the channel gets very confused.
   
   

Is there a way to write these longer scripts without using the UART?