MongoDB switch to smallfiles
Straight to the point? The smallfiles option doesn't help. It doesn't automagically shrink existing files. All this option does is changing the behavior of how data files are preallocated.

Usually, the first datafile allocated has a size of 64MB. The next has 128MB. This doubling goes on until 2GB are reached. After that, every new datafile is allocated with 2GB.

The smallfiles option simply sets the initial size to 16MB, and the doubling starts from there.

You need either to increase disk space or start to shard.