Which is more respectful, honest criticism or a pacifying lie?

Last night I got pulled into a fight about religion and atheism with someone I care for very deeply, and who cares for me. Much was said that probably should not have been, and both of us were guilty of letting anger dictate our handling of the discussion. The main source of the disagreement was my - totally acknowledged - lack of respect for religious beliefs, which I consider no less foolish (and far more dangerous) than belief in astrology, ghosts or the Evil Eye.

The person I argued with is not devoutly religious, but has never entirely shaken off their rather puritan christian upbringing. They've known for many years now that I'm an atheist, but until yesterday our conversations on the subject had been limited to the occasional reproachful remark when I was too openly disdainful of religion in their presence.

The argument was not even about christianity in particular - I actually suspect this person knows specific religions are intellectually indefensible - but about my lack of respect for what people of all religions sincerely believe; this person is concerned for my safety, believing I may be at risk of drawing real-world ire from certain religious factions I have written about, both here and in other places. This person is liberal in most ways and certainly doesn't take their morals from any holy book; I can discuss almost anything with this person calmly and rationally, even if we disagree completely... but when it comes to religion, alone among all other human sillinesses, this person just wants me to shut up.  It became so strange I can only express it by quoting the brilliant and ever-eloquent Douglas Adams: "Here is an idea or a notion that you're not allowed to say anything bad about; you're just not. Why not? Because you're not!".

I'm always wary, in the aftermath of an argument in which feelings have been hurt, of the risk of digging in deeper to one's original position to avoid having to think that maybe the criticism was warranted - of rationalising what one said or did after the fact. I don't think I'm guilty of that in this instance, but if you think I am do feel free to tell me so in the comments; the fact is that I'm NOT totally certain how objective I'm being here:

I sincerely don't think the way to show a person respect is to fake respect for their foolish beliefs.  The person with whom I had the argument last night is exceptionally intelligent, and far more educated than I am; for me to decide for them that they couldn't handle what I had to say about one of their beliefs would be breathtakingly condescending, unspeakably arrogant.

Of course, not everybody in the world is comparable in intelligence to my interlocutor from last night (in fact, statistically the vast majority are not), but when did one's right to hear an honest opinion depend on one's intelligence anyway? Where's the cut-off, do we consider you incapable of coping with facts and our honest opinions if your IQ tests at - say - 120 or less?  What about educational level, how many GCSEs and A Levels do you need, which Universities qualify you for honest feedback on your beliefs?

Something I occasionally find irritating about atheists - open ones, I mean - is our tendency (some of us are more guilty of this than others, of course) to consider ourselves more intelligent than believers. Yes, there are a few studies that support this in a very minor way, but even of these the most marked average difference I've ever seen reported is ten or so IQ points. When you're dealing with a species of which some members have IQs of 20 and others have more than ten times that - and when you're dealing with a system of measurement which is itself acknowledged to be an imperfect measure of intelligence - such a minor trend is all but meaningless.  I am an atheist and I score relatively highly on IQ tests - but that does not leave me safe to assume I am more intelligent than any religious believer I encounter, because the statistics simply don't support that.  We'd probably be marginally safer guessing that we're more educated than believers - there is at least a relatively objective measure for that - but again the existence of renowned scientists who're also religious, and of people like my conversant last night, show that we'd be very, very foolish to make any assumptions of that kind.

Here's the heart of the problem for me; I simply do not, cannot, see anything in religious beliefs deserving of anybody's respect.  When a person tells me that I "ought" to show respect for those beliefs, I am put in an impossible position; I can either be honest and disrespect the beliefs, or I can lie and disrespect the person.  When the person in question is someone I already respect deeply, this is troublesome and upsetting - and leads to what happened last night.

This is the first time in my experience that what I say about religion has led to serious disagreement with someone I love - or at least, the first time it's become genuinely acrimonious. Has anything like this happened to anyone else? How do/did you handle it? Is my position on respect reasonable, or am I rationalising? Can relationships be repaired after something like this?  I'd love to have input from other non-believers because this has hurt me considerably, in a way no amount of ranting from religious people (or other atheists, I suppose) over the internet ever has.