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The idea of "conscientious objection" has a long and complicated history in the United States (believe it or not!). Though I'm not a Civil War expert, I can talk about the changing attitudes toward military service through the 19th century, and how they had evolved from earlier models.

To make a long story short: yes, there were conscientious objectors during the Civil War, though they were unlikely to be termed as such.

The American model for military recruitment had always been fairly complicated. Because of notions of constitutional balance and the perception of political threat posed by standing armies, it was (and remained until World War II) politically unpopular to support any kind of permanent standing force. Before the War of 1812, the US army had a paper strength - essentially congressional authorization for a force - of 25,000 men. That had been raised from an authorized strength of 6,000 in 1805.

However, and aiming toward the point of your question, the paper strength seldom reflected reality, and the army was undermanned throughout the entire war.

The bulk of the service was performed by militia during that conflict, as opposed to regulars. At the time, those were primarily the two modes of armed service in the United States: the regular army, and the militia.

The militia was intended to be "the body of the people in arms" and was meant to be comprised of men of interest serving selflessly without regard to compensation, but out of a sense of patriotic ardor. To be sure, there were many men for whom this was exactly the case: Robert Lucas, an Ohio politician, for instance, gave up a position as a general in the Ohio militia to serve as a scout and private volunteer under William Hull, among many others.

The reliance on the militia goes back to well before even the Revolutionary War, and many states had laws that allowed men to object to service on religious grounds. Those were generally done fore whole groups of people, like Quakers in Pennsylvania. However, they were required to compensate the state for their lack of service int he form of pay.

Outside of religious objections, men were also fairly universally expected to furnish replacements for their own service, though the whys and hows varied by state. It was common for men who had positions or duties that required attention in time of war or crisis to opt out, and to either pay a fine or furnish a replacement.

The system, as you might expect, was commonly abused. Notions of social or cultural degradation - a kind of "back in my day" assertion - were rampant in the politically divisive 1790s, with men accusing the younger generations of squandering the "gifts of liberty" won by men more interested in liberty. The notion of interest was paramount, as the more interest a man had in his home region, the more duties it conferred along. Shirking their duties was a sure sign that the privileged classes no longer bore the kind of interest that men in earlier generations held, and that in turn fed beliefs that society itself was disintegrating.

It gets pretty wild, as you can see.

Militia service in the War of 1812 is complicated, especially by th epopular notions that the militia was running around left and right refusing service on constitutional grounds. This could qualify, to an extent, as "conscientious objection," but there is, unfortunately, very little written or examined about these men in these specific circumstances: but luckily this is my topic of particular interest.

Though the vast majority of militia refusals to serve or invade are problematically aligned with party ideologies or constitutional objections, most of them have much more to do with bad leadership, poor supply or logistical support, or local circumstances. After the war, these refusals became popularized and politicized, used as evidence of social degradation and insufficient patriotism, et al.

There was a single example (that I've found) of a group of men refusing to volunteer for a projected attack based on specifically moral grounds. It was the New York militia, who refused to accompany General Alexander Smyth on an attack into the Niagara region in 1813.

This is at the root of the problematic use of the militia: officers, even regular officers, had to ask for volunteers on any duty that was considered outside the scope of normal militia service. Regardless of the letter of the law or the personal feelings of the officers at the time, this was the standard protocol for working with militia: ask for volunteers, and threaten censure or punishment if not enough would step forward. The fact that many thousands did volunteer further problematizes the "useless militia" mythology that hovers around the war like a vampire bat.

Anyway. Smyth was an unpopular officer and a bit of a braggart, and he wrote a bombastic call for volunteers, which he had published in a local newspaper. It was chock full of the kinds of patriotic blandishments and popular rhetoric you'd expect, and it reflected, to an extent, Pickering's notions of social degradation:

In a few days the troops [regulars] under my command will plant the American standard in Canada. They are men accustomed to obedience, silence and steadiness. They will conquer or they will die.

Will you stand with your arms folded and look on this interesting struggle? Are you not related to the men who fought at Burlington and Saratoga? Has the race degenerated {emphasis mine]? Or have you, under the baneful influence of contending factions, forgotten your country?

Balled up here is basically 40 years or so of criticism of the militia system and of the opportunity it gave men who refused to serve a platform for doing so. They were free, of course, to do so, given how the system worked: but doing so might just prove how low and degraded they were as men.

The men of New York, though, actually responded and give a rather cogent counter-argument, and it is worth quoting at some length:

The clamor of avaricious traders and of factious office seekers trouble not our quiet. It reached us but at the period of the elections, and it was then but like a blast of win on our lakes, variegating but for a moment in the placid uniformity of the surface.

Why should our swords be drawn in redress of grievances we have never felt, or which if they exist are beyond our reach? Why appeal to our valour for the destruction of our own happiness or that of others?

We are the descendants of the men that fought at Bennington and at Saratoga. The labors of the field are proof alike against degeneracy and the rage of contending factions. You, General, have been more exposed to their influence. The men who fought at Bennington and Saratoga fought for the liberties of their country. Foreign mercenaries had set foot upon the soil which their hands had redeemed from the desert and rendered fertile; they had entered the sanctuaries of their wives and children. Our fathers fought and conquered. You, General, who are taking the place of these mercenaries, cannot appeal to us.

The renown which you seek is not our renown. It is the renown of Europe not of America. The wrath of God precedes it, and desolation follows in its footsteps.

Much of that passage reflects some popular notions of the War of 1812: it had been declared by the US against Great Britain, fought over grievances not felt by many and urged by party and faction for personal gain and ambition. Smyth happened to emblematize many of those issues.

As stirring and as florid as that passage is, it can only serve to reflect a minority of opinion. It does, however, highlight the deep unpopularity of the war and the frank opposition to aggressive warfare as a whole felt by many Americans.