Bacteria trapped in crystal inclusions found 'alive' after 50,000 years - what were they eating all that time?
The question is interesting, but I must say it is too early to say anything. But let me tell you what I can.

Dormancy, first of all, is a state in which all metabolic activities of an organism temporarily stop or slow down, and when saying all, I literally mean it. Dormancy can be considered, in layman's terms, as molecular level of hibernation. Any organism, in dormant state, does perform all kinds of activities, but in super slow motion. Again, we don't know anything about those microbes, so I can just tell the currently known mechanisms by which those microbes could have survived. Gypsum i.e. $CaSO_4.2H_2O$ contains sulfate ($SO_4^{2-}$), so those microbes (let me call them X from now) must be sulfur metabolizing ones to survive. Now, known mechanisms of sulfur metabolism include:


sulfur oxidation
sulfate reduction
sulfite reduction


which are summarized as:

source

Now, with sulfate already available from gypsum (considering dissociation) as:

$CaSO_4.2H_2O \rightarrow Ca^{2+} + SO_4^{2-} + 2\hspace{1mm}H_2O$

The reactions it can perform are sulfate reduction and sulfite reduction. Some of the mechanisms are:

source

In the presence of $CO_2$, glucose can also be formed as:

$12\hspace{1mm}H_2S + 6\hspace{1mm}CO_2\hspace{1mm}\rightarrow\hspace{1mm}C_6H_{12}O_6 + 6\hspace{1mm}H_2O + 12\hspace{1mm}S$

The required $CO_2$ might come from respiration. During dormancy, this process is highly slowed down, so that X may have survived such a long time by just this process.

Again, this is just the known mechanism, X may have evolved other, possibly even more efficient, mechanism. The above example was just to suggest how X could have survived in gypsum crystals for as long as 50K years. We don't know anything about X yet. From the article you cite:


  If confirmed, the find is yet another example of how microbes can survive in extremely punishing conditions on Earth.


meaning we don't even know yet whether they are really viable or not.


  The life forms—40 different strains of microbes and even some viruses—are so weird that their nearest relatives are still 10 percent different genetically. That makes their closest relative still pretty far away, about as far away as humans are from mushrooms, Boston said.


Now, viruses ain't alive. And 90% similarity means a lot of difference, which means they almost certainly have different mechanisms for survival. At last, I would again remind that it is too early to say anything unless some scientific studies are performed and published.

P.S. talking about energy source, even the heat and radiation from environment could be used as a source of energy. Obviously, harnessing energy directly from external heat is pretty difficult, but when one finds fungi using radiation for growth, then you never know!