Praise be to Allah, the Lord of the Worlds.
Performing two prayers because of rain is among the concessions granted by Islamic Sharia. This is confirmed in the Prophetic Sunnah through Hadith of Ibn Abbas (May Allah be pleased with them) who said, “The Messenger of Allah (PBUH) observed the noon and afternoon prayers together, and the sunset and Isha' prayers together without being in a state of fear or in a state of journey.” {Muslim}. Combining two prayers because of the rain has been confirmed on the authority of Ibn Abbas and Ibn Umar (May Allah be pleased with them), and this opinion is agreed upon by the majority of the scholars. In their Fiqh books, these scholars have mentioned the conditions for combining two prayers, and they boil down to four:
1-Making the intention to combine the two prayers during the first prayer, and at the beginning of the second.
2-Rain fell at the beginning of both prayers.
3-The rain wets the praying person`s clothes i.e. he faces hardship in going to the mosque because of it.
4-The two prayers are offered in congregation at the mosque. In addition, the permanent Imam of the mosque is the one who enjoys the authority to decide whether the conditions for combining the two prayers were met or not, and none of the prayer performers is permitted to make any objection. In principle, an Imam must have acquired a great amount of the Sharia science enabling him to settle that matter. Moreover, opening the door for debating will definitely be chaotic, and over what: "rain", a blessing from Almighty Allah.
However, in case one of the prayer performers had an objection, then he should discuss it with the Imam in a polite and brotherly manner to avoid creating a scene and causing sedition. According to scholars, enjoining kindness and forbidding inequity is permissible with conditions; some of which are: 1-It doesn`t cause greater damage. 2-There isn`t a considerable disagreement about the matter which is being enjoined or forbidden. 3-The inequity is expected to be removed by forbidding it.
As for the third question, we have stated earlier that the prayer performers aren`t obliged to draw the Imam`s attention openly; rather, it is permissible, but the maximum they could do is exchanging views with the Imam about his choice with regard to the issue of combining the two prayers. Hanabali jurisprudents have added severe wind and cold as valid excuses for joining Maghrib and Isha` prayers. Therefore, before objecting to the Imam`s decision, the praying people should dwell upon the evidence that he had produced, then advise him with wisdom and fair preaching along with producing their own evidence.
Not praying the second prayer with the Imam, and offering the Sunnah of the first prayer at a certain part of the mosque will definitely send a clear message. And Allah Knows Best.