help me understanding transporters

[Antares]

I have just seen the Voyager part about the Omage particle and it is really confussing me.
A brief summary:
Voyager on its way home finds a special particle which the federation consideres the most dangerous stuff in existance (it destroyes subspace). Once it a single particle of these was created by federation and destroyed a hole sector’s subspace, the borg failed to stabilize it and now several million of those damn things are right in front of Voyagers nose. A pre-warp specie did this miracle and were able to contain it.
Janeway (who obeys the orders of federation) wants to destroy it but 7of9 (which calls this particle THE perfection) first wants to understand and later to stabilize it.
Quite ok till now.
But then the confussing stuff begann. 7of9 created a special chamber in which it should be destroyed (stabilized) and the particles were beamed onto this chamber.
I mean .. WTF !?!??!
“Beaming” the most perfect particle ??!?!?
Häääää?

As far as I know there are two understandings of “beaming”:
1.The matter being beamed is destructed in one place and reconstructed at another
2.The matter being beamed is really transported from one place to another

If 1) is right, then this part of the voyager series is the most pathetic one I have ever seen. Everyone failed creating omega particles, but transportes have no trouble with destructing it and reconstructing it.

Because 1) is so ridicules and really wouldn't make sense at all, only 2) can clean this mess up. Transportes DON’T de(recon)struct matter, but really transport it.

In any case "beaming" includes a detailed analysis of the matter being transported. So why isnt the federation just using the transporterlogs to analyse the omega particle? Or why arent they just storing those particles in the transporterbuffer were Scotty remained for more than 70 years till he was found by the Enterprise D on the Dyson Sphere?

Another point that always confussed me, is the disease/injuring stuff in connection with transporters. Again if 1) would be the truth, then curing diseases with medicaments is idiocy. Just the the one infected through the transported, get all the bacterias/viruses or whatever cases the disease from the transporterlog and just DON’T reconstruct that matter while rematerializing.

I just don’t get it. Can anybody clean this mess in my brain up please?
Do I have a point when I am saying that transporting like it is seen in Star Trek cannot be like 1) and MUST be 2)?

Thanx in advance

[Natorgator]

I was under the impression that the transporters actually turn the matter into energy, then actually transport it somewhere else. So I think 2 is correct?

[Cryllin]

If they convert the matter into energy and then the energy into matter again, by being able to transport it wouldn?t they also be able to replicate it easily , because form the way I understand it , replicator technology works in a very similar way that of transporter technology.

So Natorgator I don?t think It could be the number two possibility..

Though I think the wisest thing would be to just pretend voyager didn?t happen, I try to all of the time because Janeway still frightens me.

[General Zod]

in order to replicate certain materials though, they need to have the raw elements on board to synthesize. (gotta get the matter from somewhere). Since the omega molecule would be so incredibly unique, they likely wouldn't have the components capable of synthesizing it. Same with replicating a human, there's just too much complexity for replicating one from scratch. although they have abused the transporter's capabilities in the past through certain writers. . . .

[Cryllin]

Ya exactly which is why there was two rikers ?

But yes most likely they would need some raw materials to create this omega particle.

But it seems the transporter / replicator has been abused so much in the past by various writers its hard to gage exactly what they can and what they can not do.