It's not apples and oranges, it is a logical comparison. To explain...

the whole issue comes down to authority during an emergency situation or in response to a threat. Confiscating property is justified (by police officers and by military officers) when such action is part of a response to a critical situation.

A police officer may confiscate a gun from a suspect in order to get control of a situation just as Union officers confiscated slaves from rebelling Southerners in order to win the war.

This right of confiscation, however, is not used against people who are not breaking the law or opposing federal authorities. In other words, a police officer could not legally, or justifiably, take away a law-abiding citizen's gun simply because he wanted to, just as Lincoln could not have freed the slaves of loyal Unionists even if he wanted to.

Both acts of property confiscation (by police officers and by Union officers) were in the specific context of responding to and handling dangerous situations.

As a police officer, you could only confiscate a gun (or other property) from a citizen if you could justify it on the grounds that such confiscation was necessary for public peace, safety, etc. You could not arbitrarily take away someone's property rights simply because you wanted to (ie. you could not enter someone's house without reason and remove their guns or other property because you think that guns are "bad.")

Similarly, Lincoln did not have the authority to confiscate or free slaves of loyal Union citizens, even though he felt slavery was "wrong." He only authorized the confiscation and freeing of slaves (property) who belonged to people rebelling against the government, particularly because slaves were used by the Confederacy to produce goods and supplies for the war effort against the Union. Thus, there was a practical necessity for denying Confederates their slaves---a necessity not found in areas loyal to the Union.

Does that make sense?