Overall, what you have written is understandable. It may not be 100-percent native natural, but it gets the point across, and there's nothing impolite or offensive in it.
That said, I'd make a few changes.
1. 「いつもお世話になっております。 (Can I say this to a temple???)」
For your situation, いつもお世話になっております might be a little confusing, since it implies some sort of preexisting relationship between you and the other party, or at least the organizations you both belong to. So if you were to say いつもお世話になっております when speaking to someone at a temple, the impression they would get is that you, or someone from your company/school/family etc., has contacted the temple in the past, and so wondering about that might distract them from focusing on the current topic you want to discuss.
Personally, I'd probably open with 「すみません、うかがいたいことがあります」 ("Pardon me, but I'd like to ask a question").
2. 「よろしければ 今週のある日お寺に参拝させていただきたいんですが。。。」
I'm guessing you want to say you'd like to visit on a day this week, in the sense that any day this week is OK for you. In that case, just 「よろしければ 今週以内に参拝させていただきたいんですが大丈夫でしょうか?」 would be clearer. 「今週のある日」 sounds more like you already have a specific day in mind that you want to visit on.
Also, while it's not unusual in Japanese conversation to let the end of the sentence trail off and leave the question itself unspoken but implied, communicating like that can be difficult to do over the phone, where the other person can't read your facial expression and other non-verbal cues to see that you're done talking and waiting for a response. So to keep things clear, over the phone you're probably better off verbalizing the question, like with 「大丈夫でしょうか?」
3. 「何曜日が都合がいいでしょうか?」 This is understandable, but 「何曜日は都合がいいでしょうか?」 is more natural-sounding.
4. 「本当に感謝しています」 Again, this is understandable, but 「ありがとうございます」 is more natural. 「感謝する」 is more commonly used for large or long-term kindnesses that are already being/have been rendered. At this point the temple will have, at most, agreed to let you visit and set up a time, so 「本当に感謝しています。」 feels a little out of proportion, and might have the other party thinking that you're under the impression that they've agreed to some especially large accommodation, and perhaps something larger than they're actually offering.
Again, nothing in your original draft is impolite, and it's all understandable, but these changes will probably make the conversation a little smoother.
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