In the Chinese consciousness, Buddhism and Islam are both considered indigenous, and in fact Chinese Muslims have been disproportionately represented in the military for centuries. Therefore, any nationalist religious persecution in China can only target Christianity.
Chiang Kai Shek was himself a Methodist (but judging by his record of governance it isn't obvious), and then merely because his in-laws insisted. Chiang had great plans to crack down on corruption for after he won the civil war (of course corruption was by far the biggest reason why he lost). I suspect that some of his more nationalist entourage such as Li Zhongren would have used this crackdown to whip up anti-Christian sentiment, which Chiang would be forced to balance off against the US support. It's plausible that Chiang would be removed by coup and replaced by more hardline nationalists who stage a full-scale anti-Christian crackdown, but the details are too hard to imagine.
But I think this thread is better in Future History. In modern day China, nationalism is on the rise and much of the population continues to be resentful against western powers. To its credit the CPC has done much to suppress such sentiment given its foreign policy with the west. I dare say that if China were to begin democratizing tomorrow, a lot of this suppressed sentiment and nationalism will explode. From my experiences in China I think many people are passively upset over pushy Christian evangelists. Combine this with the ongoing resurgence in Chinese religions, and if this is combined with a democratizing political climate, this conceivably results in open and widespread anti-Christian sentiment in a democratic society. It will likely be on par with Islamophobia in the west nowadays, but the specter of religious hatred by Buddhists and Taoists seems rather real and bizarre.