Or must I ship ISQL.exe with my application and INPUT scripts?

Even if you do that the dependency issues will be a right pain, it'll be a lot of hard manual work to put the scripts together and test them.

What's missing from most (all?) database engines is a version control system integration and a single command which says "update all the various bits of this database to match what's changed in the version control system" without the user having to worry about the dependencies, which really are a database internal gubbins issue that the database should look after.

-- 
Tim Ward