Governors and Presidents have the constitutional power to veto legislation funding programs that he/she may not agree with.
Perry didn't veto the funding because he doesn't agree with the agency that was to receive the funding. He wanted one person gone so he vetoed the funding until he got his way. Yes, the legislature could have overridden his veto. But that doesn't change the fact that he used his veto to try and make a personnel change. Unless it's an executive agency personnel issues are none of his business. The person he wanted gone was a Travis County elected official. That's not his call to make, it's up to the voters of Travis County to make that change.
When elected officials do things which embarass the office they hold and are unwilling to resign in disgrace, extraordinary actions are required.
Take it from someone living in Rob Ford's town. The call to wait for the next election and let the voters decide is sometimes not enough and other members of government need to go outside the bounds of normal activity in order to deal with them.