There are two ways to interpret these rules.
It comes down to how you read the header. Does the header describe the immunity and the following text clarifies it? Or is the header a name for a section of rules text?
Under the first interpretation you would read the rules as follow:
The Deity is immune to Transmutation, [such as] polymorphing, petrification, ...
The Deity is immune to Energy, [such as] disease, poison, ... [beginning at rank 1] ...
In this case, you couldn't target the deity with the Disintegrate spell (as it is a Transmutation), but you could perhaps disintegrate it through other means.
Under the second interpretation you would read them more like:
Immunity 1
A deity is immune to polymorphing, petrification, or any other attack that alters its form...
Immunity 2
Deities of rank 1 or higher are immune to disease and poison...
In this case, you could target the deity with the Disintegrate spell, at least until it hit rank 1.
Looking at Energy Immunity, I think I feel comfortable ruling that the intent of the rules is the second one. It doesn't make sense to declare the deity to have blanket immunity to all "energy," and the following text doesn't seem to be a clarification of the heading. It's just a bucket of random immunities.
Although, the repetition of "Rank 1" may mean that there's some text missing there...
I would therefore rule that Rank 0 deities are immune to having their shape changed. In the polymorph sense, not the "blown to smithereens" sense. They can still be targeted by transmutation spells that aren't related to shapeshifting, as the header is just a name rather than functional rules text.
At rank 1, they become immune to more effects, including disintegrate.
With that said... There's no official "how to interpret headings" in the rules, and it is (mostly) valid english to read them as part of the rules text. Particularly with the leading sentence under the "immunities" heading.
Appendix: Altering Forms
How on earth do you imagine a creature is disintegrated without altering its form?
(in regard to: A deity is immune to polymorphing, petrification, or any other attack that alters its form. Any shape-altering powers the deity might have work normally on itself.)
(I'm going to assume the second interpretation above from here on out, because it's the only one that applies to this question.)
Hooray for the ambiguity of the english language, I guess.
I interpret "any other attack that alters its form" as "any other attack like these that alters its form." The examples all fall under the broad heading of shape shifting, and "shape-altering" is called out in the next sentence, so I feel it's reasonable to assume that attacks that alter its form refers to stuff that turns things into other stuff.
I think we can all agree that a rank 0 deity isn't immune to being hacked at with a sword, or blasted with a fireball.
This does still leave disintegrate in a tricky position. Is it something that "blasts" its target, or is it essentially "polymorph into a pile of dust?" In the former case, you could use it against deities. In the latter case, not so much.
In favor of disintegrate as "polymorph: dust" is the fact that it's in the transmutation school.
In favor of disintegrate as "hit it until it's dust" is the giant handful of D6s used for damage, and the fact that you can actually survive it without saving.
You can go around and around like this for days. The rules don't define how much of a change is required to "change forms" officially (immunity to trimming your fingernails?). But the inclusion of disintegrate later on in the list of immunities suggests that the writer thought of disintegrate as something that "blasts," rather than something that "polymophs."
