I get the feeling you may be working in delivery or taxi services. If someone is paying you to deliver something, as long as it is not clearly illegal/forbidden and is not UN-holy water (such as cyanide to the unsuspecting or bottles of cocaine), then just deliver their package.
Unless you are living in an area with few Christians, it seems unlikely that Christians will usually ask a Muslim to do them a favour and transport holy water to a church, as most people keep their religious practices within their own circles. But if they really want you to do this, make the best choice. I am sure they can get the idea that, as a Muslim, you aren't advocating their beliefs and are just lending a helping hand. The Prophet (S) was not hostile to Christians or churches.
As for whether the water is holy or not after being prayed over, who knows. I would say that Muslims often treat certain items as holy - for instance, things from holy cities, tabaruk from majlis, gifts from pious individuals or scholars - even if there isn't any formal scriptural basis for this. In many countries, Muslims recite Qur'an over water and consider it to be helpful in spiritual healing. Perhaps the items are somehow blessed and perhaps they are not. The idea of blessing food and water through praying over it is found in many cultures and seems to be deeply rooted in the human psyche. There are certainly worse things to be transporting about, anyway, than water which someone has been praying over. God knows best.