I'm currently working on a solution for that
The chasms between traditions and denominations in the spiritual realm originate from this.
To analyze your reasoning, it seems the church acted out of fear, and was unable to demonstrate the truth with faith. Only by casting people out was it possible to stop the heresies. However, this would mean that the church had already regressed to the same state as those who crucified Christ.
I think the solution in the end is spiritual maturity, we need more of it.
There is only so much maturity one can accomplish with themselves and God, there is an implied level of maturity when the whole faith becomes one. Paul spoke of this by saying you are carnal because you say I am of Paul, and I am of Apollos but was Paul crucified for you? Etc.
So when the faith can become one again, there will be that level of maturity that was available in the beginning of the faith that gave space for the greatest and the least in the kingdom to perform some kind of miracle, some kind of healing - even if it was not their gift, for all pray, all lay on hands etc.
In John 17 I see the solution when Jesus said, may they be one as we are so the whole world knows that you have sent me. Having the trinity type oneness within our congregations as a parable is the best defense against heresies.