No, I do not see John W. Baker as being "tragically wrong", except that he overstates the "taxation without representation" factor in the origin of exempting churches from taxation. However, the idea that taxing churches would allow them to operate far more openly in promoting or opposing specific political issues is very real, though it is not scare mongering. In fact, the very fact that the IRS is watch dogging churches to make sure they DON'T involve themselves directly in political issues supports this conclusion. "Keep your mouths shut about politics, or you'll find yourselves paying taxes" is what is happening. Threatening churches with cancellation of their 501(c)(3) status is the only authority .gov has over keeping churches out of politics. If churches were taxed, that authority would go away, and churches would, indeed, have full rights to be directly involved with politics, to include endorsement of specific candidates and operating PACs. Now, I say that is not scare mongering, but OTOH, I would imagine that most liberals would, indeed, find the idea of church operated PACs to be frightening.
I bring up the ACA mandate because I see relationships in many things. Both instances are cases in which government claims to have authority over the practices of religious organizations (to include organizations operated by individuals with religious convictions.) Of course, the instances are different in detail and scope, but they still involve the same thing: government claiming authority over how religion may operate within established law.
In the case of the IRS, we have an old and traditional concept which states that government may limit the political activity of a church by withholding the tax exemption if the church gets too involved with politics. It's a claim on authority which is quite old, and widely accepted by the vast majority. My problem with this concept is the practice falls under the premise that an organization must pay taxes in order for its membership to practice the rights of U.S. citizens. (This objection, BTW, includes the political limits placed on ALL 501(c) community benefit organizations.) Seems to me the entire poll tax issue came down on the idea that the People should never have to pay for what is already their right. Yet here we have .gov stating quite unequivocally that if a church - or any other community benefit organization operating under the 501(c) tax code - that to enjoy tax free status they are giving up their rights of political discourse under the 1st Amendment promise of free speech.
The case of U.S. government vs. Hobby Lobby is a claim by .gov that secular law trumps religious convictions. It takes the position that people must give up their religious beliefs in order to operate a business that falls under government regulation. (meaning ALL businesses.) Seems their idea is if you want to fully practice religious convictions, you can't own or operate a business. If you do own and operate a business, then you have no right to freely practice your religion. And while SCOTUS did rule in favor of Hobby Lobby, when one reads the decision carefully, they did NOT actually rule in favor of religious freedom. The deciding factor was not that the 1st Amendment trumps the ACA, but rather that the state did not prove an overriding interest, ONLY due to the fact that the ACA had already granted multiple exceptions to the BC mandate. IOW, if the state CAN show an overriding interest, then NONE of our liberties are protected. Seemingly a victory, the wording of the decision states that all .gov needs to take away any of our freedoms is to prove the state has an "overriding interest" in doing so.
In short, it is all a pattern of behavior which indicates that we have no liberty except that which the government so graciously allows us to keep. This is an attitude which has slowly developed over time, but is now ripe and mature in its claim of government authority over the People. It is an attitude which must be changed.