I've read the essay and the correct answer is definitely "A government that is good at securing civil liberties will also keep religious liberties".
The Maryland farmer makes it pretty clear in his closing statement, which reads: "Civil and religious liberty are inseparably interwoven—whilst government is pure and equal—religion will be uncontaminated:—The moment government becomes disordered, bigotry and fanaticism take root and grow—they are soon converted to serve the purpose of usurpation, and finally, religious persecution reciprocally supports and is supported by the tyranny of the temporal powers".
Both civil and religious liberties need to be secured by a government. The point he's stressing in the essay is that often times religious freedom is compromised as a consequence of ineffective protection of civil liberties.
Another quote from the essay that illustrates this idea very well would be the following: "where civil government is preserved free, there can be no religious tyranny".
At the same time, the farmer cites historical examples in which an imposed religion was used by governments to persecute people that didn't share the dominant beliefs, establishing a religious tyranny that severly overpassed civil liberties. This is why the integrity of both civil and relgious freedom are unequivocally interwoven and must be protected side by side.
Hope this helps!