Seems strange that a small store would cause load problems.
Product updates do create a lot of queries on your database and if your CPU or RAM allowances are low, then it could increase the load too much.
I would do this:
1. Install a good WP caching plugin. Try this: http://wordpress.org/extend/plugins/w3-total-cache/
2. Then, increase the interval at which your store is updated. Maybe just once a week. You can do so here: The Factory > Your Store > Store menu > Basic Store Settings. Also, clicking the [Update Settings Only] button is a very "lightweight" process that doesn't create that many queries. On the other hand, clicking the [Update Products and Settings] button can be server intensive.