I can see where you're coming from but I'd argue you're comparing apples to oranges.
In 2000 there was an extremely popular incumbent who'd held off raising property taxes and was respected throughout the electorate for it. (Remember, this was *before* Mel's second term.) The NDP provincial wing were in the midst of a bitter backstabbing, infighting period following their withering defeats in '95 and '99 and in the process of running out moderates like Rae and Lankin. Federally they were not making much inroads against Chretien (their support proving to be very soft), and they'd been shut out of the mayor's office for years.
It's pretty understandable that they were demoralizing, demotivated times. And in 2000 just about every credible challenger decided to keep their powder dry.
Flash forward 10 years and all wings of the NDP have steadily been winning more and more. They've been the incumbents at city hall since 2003, learned the discipline of power, and had the chance to use it to implement some of the core issues they believe in. There's also much different, more hands-on leadership federally from someone who cut his teeth in Toronto council. And there's upcoming federal and provincial elections as well.
If I were Jack, I'd want to run a candidate in order to keep the party visible and relevant, and its messages percolating among the electorate. I'd also use this as a chance to keep my troops in campaign shape and forge more connections in ridings that might swing federally or provincially. And it would be a chance to have a dress rehearsal for 2014 when there's no more Miller baggage and an anti-incumbent campaign might get more traction.
The only challenge is finding a suitably high profile candidate to run. Pretty much by default, it's Giambrone's if he wants it.