Amnestying Bargnani puts the Raptors at approx 62 mil for the 2013/14 season with all options picked up, and at 49.5 mil for the 2014/15 season with all options picked up.
Amnestying Kleiza puts the Raptors at approx 68.3 mil for the 2013/14 season and 61 mil for the 2014/15 season.
So, as I stated before, using the amnety on Bargnani leaves them more wiggle room under the tax to make moves this year without exceeding the tax. This doesn't mean its easily done, but it does give them more room. Staying under the tax this year (with a little more room to make a move) means potential future years of exceeding the tax with a smaller tax hit. It also leaves Kleiza's expiring contract to make a deal.
For the 2014/15 season (depending on an additional increase of the cap), amnestying Kleiza leaves them above the salary cap, amnestying Bargnani leaves them well below the cap before considering other moves.
Toronto is offered more flexibility than they currently have by amnestying Kleiza, but not as much as they do by amnestying Bargnani both this season, and more so going forward.
As for Bargnani being traded for an expiring, that would be great and more benificial than amnestying him - but that is also far from a sure thing.
While amnestying Bargnani is not necessarily the best or ideal option (clearly getting something 'good' for him would be the ideal option) it is still an option, and it does offer more flexibility for the team (even if its small) than not amnestying him and/or amnestying Kleiza instead. Things do still change in Toronto's salary cap favor, just not as much as we may like them to.