Server crashing when indexing

I have a MySQL database with 3 around million records, which I use to create my dbsight index.

Once a week I have to completely re-create my dbsight index, because the data changes so much, many records will be deleted or amended, and there will be a lot of new ones.

The problem I have is that when I try to create the index it regularly uses so many server resources it causes resin and Apache to crash, and the indexing job is never completed.
I've tried changing the settings as much as I can to reduce the stress on the server, by experimenting with different values in the Advanced Settings screen, but nothing has been completely successful.

The only way I've found so far to stop the server from crashing is to disable Apache while the indexing process takes place. This reduces the load on MySQL and resin, so the indexing process can complete.
I don't really like doing this though as it means the sites on the server are unavailable while this happens - so I do it in the early hours of the morning and often have to stay up until 5 or 6 in the morning while I wait for it to finish, so I can re-enable Apache before going to bed.

I've come to the conclusion that the best way to solve the problem would be if there was some way to slow down the index creation process, reducing the load on the server. I don't mind leaving it running all night unsupervised if I know it's not going to crash.

Is there a way to do this by altering some of the existing settings, or is it something that can be added in the future?