Suitable DB2 Version for Windows Server 2012

Upgrade via restore is usually supported for databases two versions down, so to move from DB2 6.1 to DB2 10.1 (current today) you'd need to move to DB2 8.2 first, then to DB2 9.5, then to DB2 10.1. There are many things that have changed between all these versions, so it's very unlikely that the process will be smooth. Your best option would be to extract the database DDL statements and data, then create a new DB2 10.1 database and load data into it.

Do you just want to configure this? Or are you not averse to writing some code?

In the latter case, it should be relatively easy to write a small program that connects to both the LDAP server and the database and synchronizes the data. I've written such a thing once in PL/SQL in Oracle -- if it's possible there it should be possible in most languages and environments!