As for micromanagement, my opinion differs greatly from yours. In strategy games, optimally the winner is the one with the best strategy - the rest had worse strategies, so they lost. Civ adds some insymmetry to this by randomized maps and different civs and leaders, increasing the viability of certain strategies. In my opinion, it is only strategy that should be rewarded with victory and high scores - not empty clicks, no empty math. If micromanagement is given a big role and it is rewarded, a player may win simply because he spent several minutes doing extra clicks, while still having a worse strategy.
And as for abuse, yes, some uses of whipping micromanagement are abusing the game mechanics. Many of the overflow tricks have been fixed, but it's still possible to, for example, channel production from whips into wonders without having the usual 50% penalty by choosing the right things to build and, once again, doing one's math well. This is definitely abuse.