You are not wasting space, you're saving your harddisk's life. A 2k padding is not really significant, for example if you have 10.000 mp3s on your hdd you're actually "wasting" 20 megs.
Just imagine one day you decide to add replaygain information to all your files and without padding foobar will need to rewrite almost 100 Gbyte of data instead of a few megabytes.
Padding is not an issue on portable players too, on a 20G player you won't save place even for a single song.
(my rough calculations may be wrong, i had always problems with basic math

)
To your question, i don't know about a way to disable padding in 0.9 and curently i see no reason for implementing it