Dear Orange,
Peace to you.
An appreciation of the context of the narrative you share is extremely important, along with its premise of the dubious intent which also involved those that warred with God and the messenger.
Therefore, this verse pertains to the prophetic ministry, the prophet himself, his contemporaries and a response to his mission. The prophet was alive and present as a representative of God to make matters clear to them, despite which some decided to oppose him.
Today, there is no such prophet present. Therefore, no one is in the position to make a conclusive judgment about another's place of worship or their intention.
In my personal opinion, this verse is certainly not intended to provide a modus operandi to make personal assessments and judgments about present day mosques. Also, it is to be appreciated that in the absence of a God appointed prophet, many adherents of the mosques, despite their differences believe they are actually following the prophet.
Therefore, judgment only rests with God.
I think it far better if we take generic wisdom from verses such as 22:40 and 72.18, where we recognise that all places of worship belong to God along with appropriate devotion. We should disincline in making personal judgments about another's wider theological beliefs without knowing the clarity of the message that has reached them.
We would also do better in my humble opinion, by educating others if we feel we are in a position to do so. Many simply go to the mosque to offer their devotions to God and not to accept every sound byte that radiates from the microphones of the clergy.
I am in no doubt given my own personal experiences and the vitriolic and acerbic tones I have noted between Quranists that if there were 'Quran-only' mosques, there would still be divisions where one would accuse another of mischief.
However, if we find that such establishments are being used to incite hatred with a view to cause societal mischief, then this is indeed something we should curtail by action such as informing the appropriate authorities if possible. In such a situation, the secondary issue of congregation is least important as one would be better placed to avoid them.
I hope that helps, God willing.
Joseph.