I'm not going to try to address the "why the Church does this specific thing" part of your question, so I'll come at it a little bit sideways.
While you and I may not have the authority or responsibility of making decisions on behalf of the Church (except within the limits of whatever stewardships we hold like in an auxiliary, ward, class, etc.) we absolutely have the right and responsibility to have God confirm to us whether or not the Church is His organization and whether it is one that He endorses.
I think this is really important, because the Church is a huge organization full of a ton of people with almost 200 years of history: that means there are a lot of decisions that have taken place and will continue to take place and there are good odds that we'll occasionally run into one that we look at and think "...really? That's not the way I would have thought God would want it."
In these situations there are a few possibilities: 1) It is the way God wants it, and as imperfect humans lacking in knowledge or understanding, we just don't get the "why" yet, or 2) In some situations it may not be the way God wants it, but the Church is being administered by imperfect people who don't always get everything right.
Sometimes people disagree on which of the above situations exists. The distinction is important because it may dictate what the appropriate response for us it (for example, if we don't understand why we need to forgive others but know that that is a doctrine from God, we can pray and study to gain knowledge and testimony. By contrast, if it comes out that our ward primary president isn't following a required two-deep leadership policy, we could bring our concerns to the bishop so that he could ensure the appropriate corrections took place.) However, it is really good that even if we're not sure which situation above we're in we don't have to be to receive confirmation from God about the truthfulness of the Church and that He wants us to be in it.
So, it sounds like you're in the position where you think that the PCC coffee/tea serving is something that's actually being done wrong, while many others believe that it's being done correctly. While it's good to seek a deeper understanding of the Church and of the Gospel, my point here is that you have the right to ask God whether this Church is where He wants you and whether it's His before you understand this issue, and He can answer you even if He doesn't immediately give you understanding on this issue. As this New Era article points out, He can answer you in many ways, including with gradual bits of knowledge and testimony. For example, you can receive continued blessings from following the commandments that you keep, which you're taught in the scriptures and by the modern Prophets. You can feel the Spirit during a testimony meeting. You can find peace attending the temple or walking its grounds.
It's okay to have questions. It's okay to not understand why certain things are the way they are. It's good that you care about following the commandments. I'm confident that God cares that His children are seeking to keep the commandments and want to do their part to help ensure that the Church is perfected. And because He loves us and wants to help us, we can always pray to have confirmation about the Gospel and the Church, even as we continue to learn more about the things we don't understand or as we strive to do our part to build up the Kingdom.
(P.S. I guess I'll make one comment on the actual issue, related to Frere Rubik's comments above. I was talking to a friend about your question and he pointed out that some things in the word of wisdom are bad of themselves (or what you might call malum in se at law (a simple example: murder)) while others are bad because they've been prohibited (or what you might call malum prohibitum at law (a simple example: there's nothing inherently virtuous about crossing a street while walking on white lines, but we may decide to have laws about crossing at crosswalks)). While doing mind-altering drugs is probably malum in se, other parts of the word of wisdom (such as wine of a similar alcohol content to that which Christ would have drunk) may well be malum prohibitum). Such things that are merely prohibited, in his mind, serve to distinguish the Church as "peculiar." Rating Pending addressed this point in his answer to the original question and also pointed out the relevance of covenants, which members have made and non-members have not.)