The issue of what to do with heterodox (non-Orthodox) Christians who come to Orthodoxy has been a controversial one. There were ancient canons in the Ecumenical Councils which dealt with certain types of heretics and schismatics, but the groups they directly address have by in large disappeared (save for the "Non-Chalcedonians" and the Nestorians). Roman Catholicism and the whole mess of Protestant denominations are all much more recent than any of those canons. As it stands, there is no universal protocol for this, but a lot of varying local decisions.
The most common practice is the so called "Russian" practice, which is employed in most parts of the Orthodox world, and is found in traditional Russian service books. This meant that Catholics and Protestants who were baptized with triple pouring (or in the case of Catholic Uniates, triple immersion) were not baptized again, but were either Chrismated, or simply given Holy Communion and made to profess the faith, after renouncing their former errors. This practice is modeled after the reception rite found in the Ecumenical Councils regarding certain types of heterodox, who had not perverted the Baptismal form or grossly distorted their belief in the Holy Trinity or Christ Himself.
After a lot of going back and forth, in the 1700's the Greek Orthodox Churches began requiring reception by Baptism for all converts from western confessions (Roman Catholics, Protestants.) This practice was based on a heavy emphasis upon the writings of the Church Father St.Cyprian of Carthage (who taught clearly that all non-Orthodox Baptisms were spiritually void, and ought to be repeated), and was bolstered by a lot of anti-western feeling amongst the Greek Orthodox of that period. Presently this has been backed away from, and they generally employ the "Russian" practice, though my understanding is that in some parts of Greece and on Mt.Athos they still stick to the letter of the 18th century decree which mandated this practice, and continue to "re"-baptize.
Strictly speaking, neither practice is "bad" or totally irreconcilable with the other. In the strictest sense, Orthodoxy doesn't recognize the "as is" validity of any sacramental rites performed outside of Her fold. This is not to say God cannot do as He pleases... in fact I'm personally inclined to believe He can and does, but such things are personal opinions, not dogmatic statements. The "dogmatic reality" is that what we do know, is that there is salvation to be had in the Church, and that includes the grace of the Holy Mysteries. When the Church receives someone from a western confession by Chrismation, this is not a statement that She is recognizing the sacraments of that denomination "as is", as if they were the same as Orthodox sacraments. Rather, She is filling whatever was lacking in the previous rites - so if all that person had received was the waters of Baptism, now they are receiving the Grace of regeneration at the time of being Chrismated. This is not a whacky idea, since we read in the Acts of the Apostles that as a sign, the Holy Spirit descended upon some gentile believers, apart from their being baptized with water - afterward St.Peter argues to the Jewish Christians (who were skeptical about receiving non-Hebrews into the Church) that they have no right to withold the waters of baptism from them...though the truth was, this could have been at that point, only a formality - "proper decorum" so to speak.
I've struggled with this idea a lot myself, though in the end, I think it's quite apparant that in principle the Church could (if She saw some advantage to this) choose to Baptize everyone who comes to Her, even if they came from a heterodox confession which maintains a basically "Orthodox" manner of baptizing. However, historically the Church has not seen an advantage in doing this; actually it is quite rare for the Church to opt to baptize converts from heretical Christian bodies when She didn't absolutely have to. If there was an acceptable form of baptism in the former group (indeed, even some Chrismations and even ordinations were accepted - heterodox priests being received simply by vesting by their new Bishop and concelebration), then the Church's instinct has typically been to receive them by some more lenient means.