Parris is worried that the town is becoming dissatisfied with the execution of its citizens: particularly when those executed are "people [who] have great weight yet in the town" (Act Four). Parris is arguing with Hathorne and Danforth, telling them that they should "postpone these hangin's for a time". Here's the full speech you refer to:
Now Mr Hale's returned, there is hope, I think - for if he brings even one of these to God, that confession surely damns the others in the public eye, and none may doubt more that they are all linked to Hell. This way, unconfessed and claiming innocence, doubts are multiplied, many honest people will weep for them, and our good purpose is lost in their tears.
If people are executed after they have confessed to witchcraft, then "none may doubt that they are all linked to Hell". But, if people are executed unconfessed and claiming innocence, then the other townspeople doubt how just the trials were, and discontent is bred. The people cry, and lose sight of the "purpose" of the trials.
And what is the "good purpose" behind all these executions? To wipe out the witches and witchcraft from Salem, and to turn it back into a noble, Christian community. But, of course, when people are being executed, the politics within the town have to be carefully managed - as executing people isn't the most Christian thing to do, per se. And this is what Parris is arguing about.
Hope it helps!