Can New Blog Templates ignore certain settings?

I have a plugin that also hooks into the new blog creation process and we both collide. The only thing my plugin does is adding a wordpress option into to options table with a option_name and option_value for the newly created blog. These are overwritten by New Blog Templates (as they should), I want to keep every other option that is present in my blog template but this one single field I would like for New Blog Templates to ignore.

Is this something that can be modified in the plugin code or am I left to my own devices?