We had the 2005 model, just sold it off last month. Its engine lost most of its potency around the 170k km mark, around 100k km run on CNG did it in I think.
Either way, upon looking at all pros and cons, we went with a complete replacement and it breathed a new life into the car. The way we saw it, an engine assembled and packed by Honda themselves would suffer from less quality control issues, considering the innards of a Honda engine are rather fine tuned if not delicate. Fitting the ready to go engine only took a day or two, much more convenient than an overhaul.
The flipside was that we had to change the engine number on the book, which we frankly didn't deem as valuable as having a fit engine that would last us in the long run.
The engine ran like a dream, fuel economy was top notch and just felt and sounded like a Honda engine should. On top of that intangible satisfaction of knowing your engine was put together in a Honda factory, the hassles of engine dismantling and assembling were avoided.
If there was a small engine part that needed replacement, I would be ok with replacing a piston/ring or whatever...but if it is a complete overhaul that is required...go with the sealed engine from Honda. My mechanic was from the Honda Pit Stop in Cavalry Lahore, and the car was maintained by them as well.