We have a similar project structure: shared database with both java and rails applications as clients. I advocated and got buy-in to use the rails migration mechanism for handling database changes. It takes a bit of rails advocacy, and some willingness to help but the java team is also writing their own migrations.
We have some cases where we use stored procedures and database specific column types, so we changed the rails environment.rb to use sql for creating the test database.
# Use SQL instead of Active Record's schema dumper when creating the test database.
# This is necessary if your schema can't be completely dumped by the schema dumper,
# like if you have constraints or database-specific column types
config.active_record.schema_format = :sql
On the plus side managing the sql with migrations makes rails testing and setup clean for you. The downside is that some of the migration files are just not that pretty (e.g., you can't use the migration DSL to generate stored procedures so you have these execute %{blah } in your migrations).
Just remember to keep communication lines open beteen the teams. I like the fact that "cap production deploy:migrations" makes updating the production database dead simple.