How do I fix the currently installed Ubuntu without overwriting/erasing the left over files (from rm -rf command)?
If you ran
rm -rf from the root directory and let it run to completion, you will have a blank partition. Any chance to recover files (see Best tool to recover removed files) would have to be done while running from a LiveCD.
I am assuming you are talking about a ext4 partition. The biggest issue you will have is finding the exact files to restore, as the names of the files will be lost (unlike the FAT32 file recovery). Some of the recovery tools can search for patterns that certain files types have. For example, all jpg files have parts of the file that share a common binary pattern. You can tell a recovery tool to recover files with that pattern. You maybe successful at recovering some files that way, but as for restoring you entire system, your best bet is to reinstall, as you will not be able to provide file names for all of the files that were deleted.
Is using boot-repair safe?
I am not familiar with boot-repair, so I can not give you definitive answer here. Since you have deleted your entire Ubuntu install, I would go with the reinstall.
Is there a way to directly go to Windows 7?
Best way to do this quickly is reinstall Ubuntu, it will fix grub so you can boot windows.