Here's a response I wrote to a comment on somebody's blog. It still needs work, but the rewards of that work are less than the cost in time and effort, so I have no incentive to improve it further. But I think it contains enough good ideas that I don't want it lost forever to history, so I'll quote it here for my own future reference.
On the other hand, there's something I've been paying more and more attention to that is somewhat troubling. I never realized how many concepts in the Torah we've basically written off as not relevant. Shmitat ksafim (and the debate about shmitat karka), the prohibition on interest, even the need for two witnesses and warnings for capital punishment (see Drashot HaRan on Shoftim). I completely understand the need to adapt - and I do identify more with chazal's takanot. But on the other hand, if the social and legal structures in the Torah aren't relevant, and couldn't predict the life we live in now - than why should the ritual ones have such power?
Change of custom in itself is not a theological problem. Custom naturally develops over time; were that not the case different customs regarding a single issue would never exist.
One real value of customs (and ritual mitzvot) is that that they provide a sense of continuity. Ideological movements (romanticism, communism, the Enlightenment) rarely remain popular for more than about a century, whereas religions routinely last for thousand of years. That's the case regardless of the truth of the ideology/religion. The emotional resonance of customs and rituals is one big reason why. By lighting shabbat candles, we help ensure that our great-grandchildren will follow our ideals of morality. For that purpose, it does not matter if the manner of candle lighting changes a bit over time, nor that we recognize that such changes can and do take place.
Obviously, though, any explicit mitzvah which has come to be neglected should be observed according to halacha. Halachically speaking, a "minhag" which contradicts halacha is not a valid minhag. Practically speaking, in cases where custom contradicts halacha, that custom is objectively acting against and not preserving that aspect of halacha.
When God commanded us to use edim, hatraah, and so on, He knew that this would not be sufficient for conviction in many cases. If the best solution available is to use secular power to punish as well, then that is how God would have wanted us to act. God presumably intended for us to punish criminal by any possible legitimate means, so the secular judgment expresses His will as the beit din's judgment would have.
Concern about the "relevance" of a mitzvah is a theological difficulty which follows from a more fundamental theological difficulty: doubting God's omniscience and/or the truth of the Torah. While most of us have had these doubts, they are an issue to be recognized as problematic and worked on. Of course it immensely helps to realize that not all Divine will is expressed in legal statements (as one example "gadol shimush talmidei chachamim yoter melimud torah"), and that God doesn't hold it against us if we try our hardest, yet the Torah's vision of society is not achieved.
An instructive parallel is the issue of haaramah, where we mostly say that is OK to "trick" God (i.e. mechirat chametz), because after all God knew about the halachic loopholes when he gave the Torah, and implicitly allowed us to use them. Here too, a correct perception of God's powers and role nullifies concerns we might have about halacha's implementation.