Making things worse
There's one other controversial point that is still worth investigating. Condoms, Cardinal Trujillo says, far from preventing the AIDS epidemic, may have actually made it worse.
Cardinal Trujillo says that safe sex campaigns which promote condoms lead people to think they're completely protected when they're not
"There is a good reason for a clear-cut prohibition against condoms," the Cardinal told Panorama last year, "far from stopping AIDS, they have encouraged promiscuity, leading many more people to get the disease."
As supporting evidence Cardinal Trujillo cites a paper by Professor Norman Hearst, Professor of Family Medicine and Epidemiology and the University of Califoirnia. He's studied AIDS across the world - including Uganda and Brazil.
Dr Hearst told Panorama that, contrary to the way Cardinal Trujillo has cited his research findings, there is no conclusive evidence that increased condom use leads to increased promiscuity.
But the Professor believes Cardinal Trujillo is right to question whether condoms are working against AIDS.
In some parts of the world, he says, they are not fulfilling the hopes so many have placed in them.
Hearst is one of a minority of experts who have begun to question the value of condom promotion in AIDS epidemics where the virus is being spread in the general population.
Other scientists who agree include Harvard's Edward Green, former WHO scientist Rand Stoneburner and his colleague Daniel Low-Beer of Cambridge University.
Their work is quite controversial and some of their most salient conclusions not generally accepted.
Hearst told us: "We know from our research that if you use condoms some of the time but not all of the time they do you little or no good."
"The concern is that we may have a generation of young people in at least some African countries growing up who have been taught to believe that condoms equal AIDS prevention and that believe they're doing their part by using condoms most of the time except when they don't happen to have one, or they happen to be drunk or they have a partner that they feel particularly attracted to or whatever."
"And that's just not going to do them much good."
"There may also be issues of the quality of the condoms may not be quite up to standards of what you or I would buy if we went to the pharmacy to get one, or the issues of storage and non-air-conditioned warehouses, there could be a lot of things but I think people need to be realistic in terms of what's really going to happen in Africa."
Dr Hitchcock however believes the lack of success for condoms in Africa is no reason to shift finance or promotion efforts to another agenda.
She said: "There may not be enough condoms to go around, or people are not using them, or people are using them incorrectly. The first is a supply issue. The other two are intervention issues."
Like other scientists and Cardinal Trujillo, Dr Hearst pointed to Uganda under President Museveni for an example of a different - and potentially more successful - method of reducing HIV rates.
Hearst said: "As President Museveni said in countries like ours where a woman has to walk 20 miles to get an aspirin for her sick child or five miles to get any water at all, the issue of a consistent supply of condoms may never be resolved."
"So if we are telling people that using condoms is what they need to do but we can't guarantee them that a condom will always be available, we may be setting them up for failure. "
Some other scientists who don't go that far - for example Professor Malcolm Potts of UC Berkeley - are also recommending more emphasis on behaviour change promotion to combat AIDS.
But all - including Hearst et al - told us they believe condoms are an essential component of an effective AIDS strategy and oppose the kind of general prohibition on condoms that Cardinal Trujillo advises.
Promiscuity and risk-taking behaviour
This is a highly controversial area fraught with conflicting data and outright speculation.
Cardinal Trujillo claims condoms increase risk-taking behaviour.
"People think they're covered and they're not" as the Archbishop of Nairobi told Panorama in "Sex and the Holy City".
But as Professor Hearst says there is no conclusive evidence.
Some scientists have calculated that given a particular failure rate with condoms, certain levels of hypothetical increased sexual activity could lead to more AIDS cases.
But we could find no empirical data to prove this is actually happening.
Others have suggested that what's called "Risk Compensation Theory" could come into play. This is the idea that people are willing to take a level of risk for pleasure or reward, and if the risk is decreased - say by condoms - they will increase it back to the predetermined level they find comfortable, knowing they can now have more reward or pleasure in return.
If they're careful and well-informed the precautions they take will give them a similar level of risk but a greater reward - this is called "homeostatic" risk compensation.
But the suggestion is that people are ill-informed about the risk because they don't realize condoms may in practice not be 100% safe, and so unwittingly take on too much risk.
It would be rather like people thinking they're safe because of seat belts and then driving faster - leading to more fatal road accidents (it has been suggested that's happened in some countries, though that's very hotly disputed).
However, once again we could find no empirical data - or firm evidence from our own reporting on the ground - to support the speculation that this is happening in the AIDS pandemic.
Condoms can significantly cut the risk of HIV infection, but are not perfect or foolproof.