If the water was black (ink like) then there will most likely be magnetite build up in the system which is a by product of the corrosion process. I would say (without having seen it) it is probably better to have it powerflushed and treated with inhibitor. It should take a full day to do a powerflush properly, hence the cost.
You can put a chemical in the system, such as Fernox F3 and leave it to work round for a couple of weeks, empty it, fill it and hot flush it out again but it may not remove as much of the deposited material as a powerflush will.
Magnaclean filters are very good for magnetite but a filter with both magnet and strainer will work better in my opinion as they will collect materials other than just ferrous.
Hope that helps?