The fourth column of `lsof`'s output tells you that this directory is the _current working directory_ (cwd) of the process. Most probably `compton` was started in this directory. Most probably you might kill the process and restart it in another directory (e.g. `/`).
You _might_ try forcing it to leave the directory with this hack:
1. Attach a GDB to the process by issuing
$ gdb -p
where `
2. Inside `gdb` issue
> p chdir("/")
> detach
> quit
`$` and `>` are the respective program's prompts.
**Note:** In case `compton` has a particular reason for being in this directory this might crash the process in a mere horrible way. I didn't find any calls in `compton`'s source code that suggest it is there on purpose, but be warned. On the other hand… this would also solve your problem. ;)