I know this thread is a little dead, but I'd still like this idea thoroughly explored without sidetracking it with talk about chunk updates and how the physics work.
The basis of using resources for fuel (mining coal, pumping oil, refining uranium, etc.) is that it provides more energy than you (the person gathering the resources) put into getting them. Oil, coal, uranium, and wood are all products of stellar fusion when you get down to it. Oil, Coal, and wood are all products from organisms that grew and sustained themselves by using sunlight to convert water and carbon dioxide into glucose, and Uranium came from the isotopic transmutation of the stellar implosion and resulting supernova that preceded then coalesced into our current star system today. Theoretically antimatter can be made if enough energy were put into the system by natural means (like some sort of stellar phenomena) then captured and contained to ration out in a reaction chamber. I can understand where you're getting this notion that making antimatter from scratch should be more costly than the energy provided by it, it should be. Getting antimatter that is readily available (or at least accessible) only costs you the necessary tools and transportation to acquire it. But I digress...
I'm all for seeing antimatter in the mod, how you utilize it and contain it is debatable. There are many different ideas people can have for it, and different ways to interpret them into the mod's balance. I suggest we follow a few basic rules to wrangle in the variety of ideas, and below them are a few game mechanics I have added as my own suggestion using these rules as a guideline. I'm not saying it has to be this, but I think they properly emulate antimatter in Minecraft. My ideas come from Star Trek's antimatter concepts, but not specifically built around them.
##Matter and antimatter will react and annihilate each other when they come in contact:
-This means if a player touches it, steps on it, hits it with a tool, fires an projectile at it, or places a block on it they should either die or be extremely hurt without specialized armor, (like the quantum suit, or nano suit) which would be destroyed/damaged instead but protect you a little from the energy released.
-Contact will annihilate the matter and antimatter in question, making you extra careful not to screw up getting it.
-Harvesting and moving it should require special tools that manipulate it in such a way as to prevent this.
-Losing containment should very catastrophic, much like an overheating nuclear reactor, but far worse. There should be no fail safes like reinforced stone in IC1 or the proposed iridium stone in another suggestion thread. You lose containment, it's like a blow out sale: everything must go.
##Antimatter should be EXTREMELY rare and inaccessible but generate huge amounts of energy:
-Finding that 1 block of antimatter in the middle of an unforgiving place like the deep (now dark and scary thanks to 1.8 ) parts of the earth near the bedrock or the ghast and lava-ridden nether should be a rewarding experience for the player, as is developing the technologies to harness it's power.
-Making even a single containment vessel should be something that requires a lot of development, we have force fields and matter generators, both of which require a ludicrous amount of resources, why not use these as a basis to guide harvesting, containment, and reactor recipes.
-The required teching and resulting energy usage should be such that it makes nuclear reactors seem like furnaces in comparison.
-Antimatter should react with matter generated by the matter generator not just anything you have at hand. A precise and costly addition to the very precise and costly work of obtaining antimatter. It certainly helps to have scrap from a recycler in this case.