I would likely put a TRIGGER on the 2000 table and insert the captured changes into an audit table, then either immediately sync the 2008 database with just those changes through SSIS ( or even a linked server if that suits you ) or do an overnight sync, depending on what would have the less impact on business-hours performance and the network as a whole, truncating the audit table on successful transfers either way. This would ensure the changes are easy to acquire and small enough to pull across the network without generating calls from your infrastructure engineers. The audit table itself could even live in a different file group to reduce disk contention if necessary.
That said, there's probably half a million ways to go about doing this, and your specific, optimal solution is going to revolve largely around the details of how your environment operates today and even the specific structure of the table in question. For instance, if the "rebuild" you've mentioned is a severe example, involving either TRUNCATE or a complete DROP and CREATE, the simple TRIGGER suggestion I've made is not going to be the solution for you without a significantly extended amount of effort, especially compounded if your source table is using an IDENTITY column.
In that case, a Lookup task in a Data Flow may seem like a reasonable route at a glance, but this effectively results in the entire table being pulled across the network anyway for the comparison. Comparison logic at this point is just unnecessary overhead, you may as well stick the receiving catalog in SIMPLE recovery mode and stage all of the data you've received on the other side of the pipe. Doing an ALTER ... SWITCH after the transfer would at least then limit the lock on your reporting table to a single meta data operation, keeping it otherwise completely available to the reports being generated from it.
