at first i wanted to suggest a way to read the inventories of machines so you can stop the flow of items into them. but then i noticed you can put comparators to the redtsone ports of them.

thing is, if you have a comparator on the redstone port, and put items in the machine the comparator will not notice that until you cause a block update.

Newest Forge and IE version

also, i'd like to suggest the idea of inventory filters. and/or advanced redstone output?
Item filters in the same sense as RFtools' Crafters have them, you basically only allow specific items to be in specific slot, so that the assembler or automated workbench (for example) cannot clog up with a single item (which would cause it to stop making stuff, which just makes it permanently stuck), and the second idea was to read the amount of specific items inside an inventory, which would also remove the possibliby of items clogging up systems, as you can just ask the amount of each item in a Machine and then turn said item off if it reaches a critical amount. (which also means no clogged up belts)