When I was in KY I had several players each year qualify for Skills USA and I let them go everytime - no harm no foul because it's a school function and they are competing to be the best of something. I don't have a problem with that. That's why we have a bench so others can stand in if needed.
That being said you're not quite in this predicament. You have no idea if your coach will be as willing to let you miss for this like I would. It seems like he would since he's allowing you to go on a church mission. But this is part of the problem too - the church mission. Don't think I'm downing you for going on the mission because you're doing a noble thing but the timing of it is not good.
This is a problem I'm seeing is that kids are wanting to be part of everything and participate in everything equally. That's not possible. I'm all for doing as much as you can but there needs to be something that is a priority. This takes precedence over anything else. Look at your things - Skills USA will be a few days, church mission will be a week but baseball season is a few months long. You have to figure out which is most important to you and focus on it.
It's nice to participate in many things but it can't come at the expense of truly knowing what commitment is. You have a tough decision to make and nobody can make it except for you. cmcconnel has given you good advice.
Best of luck