First, get your Domino Servers to R7.0.3, and FP1 is good. This should address some of the issues related to getting properly formatted calendar information out of Domino and into Exchange. And then the other trick to do (this seems contrary to any logic, but it is related) is to check the Location document of the Notes user that is sending the calendar information to Exchange. What you need to do is look at the Mail tab on the current location document and check the "Domino Mail Domain" field. The "Domino Mail Domain" field must be populated with the Domino Mail Domain for that user's Domino infrastructure, this is not the internet domain.
The Domino Mail domain is stored in lots of places, you can check Person documents in the Domino Directory (NAMES.NSF) or the Directory profile document in the Domino Directory.
It appears that without the Domino Mail Domain being identified in the user's Location document, the calendar entry that gets generated by the Domino Server to be routed out does not include the Mailto attribute for the Organizer in the ICS file.
Good luck!