Jesus says whoever believes has eternal life. Altar calls and the sinner's prayer deceive believers into thinking they saved themselves by reciting a chant and going forward. They believed and had eternal life or they would not have followed these false admonitions.
Scripture also tells us that, as ambassadors to Christ we are to plead on Christ's behalf that men be reconciled to God.
I understand that those things can be misused. But we cannot discount our "ministry of reconciliation" simply because other's have taken things to extremes.
That said, I am not sure that you and I have the same idea about an "altar call". Growing up an "altar call" was used in about every Baptist church in our area. The pastor would give a presentation of the gospel and invite people to come down to the "altar" if God was working in their lives. He would use the "sinners prayer" and say if those words reflect your repentance then now is the acceptable time. If someone came down then the pastor would keep him or her after the service and meet with them, go over the gospel message, etc.
But I have never seen the "sinners prayer" used as a "say this and you are saved" kind of thing. I have heard that it has been used that way, and if so I agree it is wrong. I do not know of many churches who now use the tool as so many have decried it's use because of it's supposed misuse.
I am not exactly sure why "altar calls" (pleading that men be reconciled with God and following up with them by witnessing to them about the gospel) is such a bad thing other than the use of "altar".