Sql-server – One table used in two databases

First there's no such thing as one way peer to peer (that I know of). Are you sure you aren't using transactional replication?

Are the deletes done via stored procedures? If so you can replicate the stored procedures as well as the tables (all in the same publication, this will require a reinit of the subscribers). This way the stored procedure call will be replicated instead of the actual row by row delete.

With only 700k rows in the table, even if you blew them all away and reloaded them the replication shouldn't get that far behind unless you have a really slow link between the servers (which you didn't specify).

There is no substitute for benchmarking. To answer the question, I would create and populate several possible tables. Then I would expose these tables to your typical workload, and benchmark.

Including additional columns in you NCIs will slow down modifications and speed up selects. Based on frequency of both, we can choose which approach uses less resources. If a row is on average read twice per year, your conclusions might be different as compared to the case when every row is on average read twice per minute.

Besides, not all queries are born equal. If some queries must complete in certain time no matter what, then you must make sure these requirements are met. Obviously such requirement trump the common good approach described above. Only you can know the actual requirements.