Yep. All we have is the default tekkit installed. I ran into the nether the other day and there was dropped gear from someone who died a day earlier. In the server we used to play on, that stuff was gone in 5 minutes. That is definitely something that tekkit would benefit from.
We do use the remove command - unfortunately the pipes bug seems to happen worst when there is no player on with a quarry (actually 6 full size ones) running at the same time. I am not sure if it can be scheduled because it is a location based command. I have run it from the console from mcmyadmin with no success. You seem to need to be a physical player located somewhere in order to get it to work.
Depending on the frequency of connection, entities can pile up to the point where it is no longer possible to log in. I have then had to use mcedit to clean it up. Right now I am failing to find something that handles auto cleanup. I have installed nolagg but I'm not convinced that even that will fix the problem as at best it will probably reduce the entity drops by a factor of 64.
Thanks for your suggestions, though.