Are you sure boot.ini is hosed? That shouldn't happen.
You didn't specify which version of windows, but if it uses boot.ini it must be either 2000 or XP. You also didn't specify which file system is being used, but probably it is NTFS.
If you cannot boot into Windows, that does not mean that boot.ini is messed up (though that could be the case); it could mean that the boot loader is now set to do linux only. I would consider this to be far more likely than the possibility that boot.ini got damaged by a linux install in a different partition.
It is dangerous to try to write from Linux to NTFS, and this is not recommended. You can use this package if you must have write capability,
http://www.jankratochvil.net/project/captive/
but again, I am skeptical that this is your problem. Please provide more information on what exactly is happening.
boot.ini is a text file; have you tried to read it with an editor (either in Linux or Windows?
What boot loader did you install?
Does that boot loader give you the option to start Windows at boot time?