This is surely due to your category layout (maybe autocreate via magmi categories plugin).
This is not "magmi" that has this resource consuming behaviour but Magento.
I suspect you have several thousands of categories to have such a slow behaviour.
I would have advised to read this article i wrote some time ago, to understand the problem.
One way to get around this would be to use full page caching to avoid magento to query the database too often, but it's only a workaround.