The political position Joko is in has played a major role to influence the decision. The arrogance towards killing them has purely political motives. If he were to send them home and alive, imagine the impression this leaves on the law in Indonesia. This will make Joko and the Indonesian law seem weak and easy to manipulate and influence by external forces (for example, the Australian government is trying to manipulate a decision here). The political arrogance is a must for Joko. His other option, letting them go and alive, can lead to damaging results politically for Indonesia.
Given how the media and Australian government has inflated the issue, this just gives more of a reason for Joko to keep the political arrogance applied to the situation. In saying this, Joko's mistake was imposing the death penalty in the first place, because the shitstorm that has occurred has left him in a position where his options are very limited. Back then the options were plentiful, but after everything has happened he can't do much without damaging the image of Indonesia now.
And for the record I have no opinion on the matter of what happens to the two on death row, as I'm not in a position to judge or make a decision.