A few reasons:
- With a time-delay, they can't be sure it went off as planned.
- Related to the first reason, what if the Kazon were able to interfere with it or remove the charge before it exploded?
- They can't be sure just how long the trip back will take. They don't have enough information to know if things like blackholes and wormholes and supernovae could change the timing of the trip home and the Voyager could be torn to pieces if the array blew up before they reached Federation space.
- Related to all the others, it'd be quite tricky to set the timing to be long enough to ensure they made it home, but short enough that the Kazon can't disarm it.
- What if activating the array disturbed time and space enough to mess with a timing device?
Put yourself in Janeway's captain's chair: If you set the tri-cobalt device to detonate after you get home, how long do you set it for? And can you be 100% sure that once you've departed, you'll have a smooth trip and it'll go off after you make it back and that nothing will go wrong once you're gone? And can you be sure that the Kazon, whom you've been fighting, won't manage to sabotage the tri-cobalt device?
The only sure way is to blow it up immediately, while you're there and can be sure it's gone.
Another point is that even a highly trained starship captain may not see every option open to them at every moment, especially in times of stress or battle. Their focus is survival and getting the job done, so other options may not have occurred to her at the time (but I don't consider this a likely explanation).