Why did John baptise Jesus...wasn't he holy already?

[Gorgias]

Gorgias,
Christ institutes all the sacraments prior to ascending, and it can be seen that in most cases this is accomplished by Him subjecting Himself to become the divine matter of the sacrament.

“Most cases”? Jesus is the matter of marriage, of confirmation, of baptism? Hmm… I think you’re stretching the point a bit too far.

John’s baptism was efficacious

The sacrament of baptism wipes away sins, justifies the Christian, and imparts sacramental grace. John’s baptism does none of these.

The argument is not that the baptisms are the same, John’s was efficacious for the preparitory requirement of repentance

Repentance isn’t a requirement for baptism. After all, babies who have committed no sin may be baptized.

That the baptism was made perfect here before the appearance of the church at Pentacost, is no less a greater mystery than that the Eucharist was divinely instituted before His sacrifice and the appearance of the church. That the commission and full form of baptism does not come until much later

The Great Commission happened well before Pentecost. The “full form” of baptism existed on Pentecost day – the account of Pentecost (Acts 2) tells us that around 3000 people were baptized on Pentecost day.

If Christ being baptised was a prefigurement, what greater and more perfect event does it prefigure and point to?

Yes, it points to the sacrament of baptism. It, itself, however, was not sacramental baptism.

The argument used that the sacraments flow out of the church, if similarly applied to the Eucharist would imply that the appostles did not partake of a sacrament at the last supper as the church had not yet been established, which is not the case as they fully did receive the body and blood of Christ before His salvific sacrifice and appearance of the church at Pentecost.

Agreed – the Last Supper was Eucharist and Holy Orders. However, it does not follow from that truth that a baptism – one not even performed by Christ (as was the first Eucharist and ordination of the apostles) – was sacramental.