I don't have a problem with the idea that Jesus existed in spiritual form pre-mortally--I in fact believe this is supported by other passages (a few examples here and here)--but I don't think that is the message this passage is intended to convey.
The context of the preceding & succeeding verses is helpful in showing that John is cautioning against a specific false doctrine:
1 Beloved, believe not every spirit, but try the spirits whether they
are of God: because many false prophets are gone out into the world.
2 Hereby know ye the Spirit of God: Every spirit that confesseth that
Jesus Christ is come in the flesh is of God:
3 And every spirit that confesseth not that Jesus Christ is come in
the flesh is not of God: and this is that spirit of antichrist,
whereof ye have heard that it should come; and even now already is it
in the world. (1 John 4:1-3)
Note that John again raises this concern in 2 John 7.
What false preaching might be in mind here? This sounds like a pretty clear description of Docetism (see here) which, in an effort to emphasize the inferiority/impurity of matter, denied that Jesus did anything physical.
This of course was very concerning to Christian leaders, since it denied both the incarnation and the resurrection.
The idea of an embodied God has bothered some people in the past and bothers many today. To borrow an effective rhetorical question from Jeffrey Holland:
If the idea of an embodied God is repugnant, why are the central
doctrines and singularly most distinguishing characteristics of all
Christianity the Incarnation, the Atonement, and the physical
Resurrection of the Lord Jesus Christ? (see here)
I can see why John in particular would be so forceful in denying this doctrine, as one who had been eyewitness to the very real physical life, sufferings, and death of His very real, physical Leader.
John's Apostolic testimony
That this is the principle John has in mind is driven home by how he starts the letter:
That which was from the beginning, which we have heard, which we have
seen with our eyes, which we have looked upon, and our hands have
handled, of the Word of life; (1 John 1:1)
The physical reality of both the mortal and resurrected Christ was a big deal for John.
The Gospels teach of an embodied Christ, and his bodily resurrection is their crowning moment. John and others (think Igantius) were very concerned by the efforts of the Docetists to deny these central claims of Christianity, and so they specifically called out the beliefs of Docetism as heretical.
Addendum to address a concern that was raised
This question takes an A=>B logical form (If A then B). I'm suggesting that A=>B is not a correct interpretation of the passage...but in doing so it is necessary to point out that ~(A=>B) does not mean B is false. If I claimed B is false my argument would be fallacious. The first paragraph of my response was intended to guard against this fallacy; I gather that this remained unclear to some readers. Hopefully this addendum provides some clarity.
A is the passage
B is fleshless pre-mortal existence
A = TRUE
(A=>B) = FALSE
B = not answered by this passage
I don't believe it would be in scope to respond to this question with a detailed discussion of my personal beliefs on pre-mortal existence. For those interested in this information, the best I can offer you is a link to my thoughts here.