There is an ongoing conversation at An und für sich which is concerned with the relationship between philosophy and theology. I think Anthony is making an interesting point that deserves further consideration.
I don’t think it is intrinsically problematic that theology has an unprovable axiom at its heart (namely, God exists). Furthermore, I think that if this axiom is made, it is worth the effort to investigate the consequences of it and its attached axioms (this God is a Trinity, he created the world ex nihilo, etc.). What is problematic is not acknowledging that such axioms make genuine dialogue difficult, though not impossible. If you start with an unprovable axiom, it is disingenuous to fault other systems (based on other unprovable axioms) for not adopting positions that support the conclusions of your set of axioms.
This difficulty aside, I think a worrying hermeneutic plagues contemporary theology. Two structural clichés dominate theology’s use of philosophy:
1) A particular current philosopher or philosophy says a, but really his argument is a weaker form of this particular theological point b. The reoccurrence of this point in contemporary philosophy shows that it is inevitable to return to the need for God in order to think the subject, language, politics, sexuality, etc.
2) A particular current philosopher is a proclaimed atheist, but if we examine his work we find underlying religious themes that prove his thought relies upon an unacknowledged belief in God.
To name these as clichés does not mean that they are never true; it just means that they are the recurring approaches that have appeared in theological appropriations of Derrida, Foucaut, and Lacan (to name the people I have had this experience with). These operations, in their frequency and seemingly universal applicability, demonstrate the strength of theology as an ideology.
For Althusser, ideology is not bad, per se, but is a necessary step in the development of a science. In this sense, I think the question facing theology today is this: is theology as a science conceivable?
I confess that I don’t have an answer to the question, but it seems that theology constantly falls victim to the ideological conundrum: ideologies are not capable of questioning their own problematic. It is only with the irruption of a science, and the changing of the problematic, that the problematic of the ideology and its tautological inertia is revealed.
I am not sure what a science of theology would look like, but I think the development of such a science must begin with an acknowledgment of the changed and changing topography of the intellectual landscape. It is striking that the confessional framework of Christianity remains stated, and thus largely argued, in medieval (or earlier) philosophical parlance. Surely there is room for interaction between theology and current epistemology, phenomenology, ontology, and ethics that departs from the above-mentioned clichés. The difficulty is arriving at a position where one is wiling to approach such an interaction without having decided all the questions posed in favour of one side or the other.