Any intensive PHP process causes a load on the server’s resources. If you are scanning a lot of files for a long time then it is likely to cause an abnormal load. If your server is not adequately proportioned to handle this load or they are trying to host too many people on a single server then they could have a problem with you taking too much of their precious system resources.
If they are really that tight about what processes you run on your site then you should probably switch to a better server. I have room on my servers to host your site and all my servers can handle that kind of load without any problems. I charge $12/month per site, if you are interested in hosting with me then I can move you site tomorrow 
Aloha, Eli
