Another way to reliably monitor it is using BFGminer (works for 32bit version only can be installed in 64bit Windows though) in proxy mode. Point your miner to the machine running bfgminer --http-port option, while pointing bfgminer to your chosen pool. Should give you an accurate picture as to how it mines. If you want to go the extra mile use cgwatcher for a much more user friendly interface to watch it with. Can even export the data and reports. That would work best for checking a sustained check. That said the web interface should be just fine to watch it also. But accurate real time stats would be better via bfgminer IMO.

I'm having a hard time figuring out what you mean by "equality of all nodes".  The equality (or inequality) of nodes is not part of the system.  No one cares about nodes.  We care about the chain.  If a node has the correct chain and can give you a copy, it is "equal" to all of the other good nodes.  If it doesn't, or can't, then it equal at all, isn't even a node.

The checkpoints do not provide any security, nor were they ever intended to.  They just keep "unequal" nodes from wasting your time with bogus chains (whether by accident or malice).

Also, you are free to edit and recompile as needed.  You can strip them out entirely, or add your own, or change them.  Whatever you want.  The reference client is written for (and compiled for) working well for a wide audience.

Technically, a longer chain is the best chain, regardless of the checkpoints.  In practice, the checkpoints are far enough in the past that if a new chain showed up that overturned one, we'd almost universally consider it an attack, and roll back.

P.S.  No one particularly likes the checkpoints, the devs least of all.  There has been much discussion about removing them, or switching to a soft system (config file, etc).  So far, no one has come up with a really good solution.