Evolutionary history: did any organs start out as autonomous organisms?
Very short answer

No!

Long answer

It is not the nucleus who was an independent organism but the mitochdonrion (organelle) (One might discuss this point and say that both are correct, it is just a philosophical issue of the identiy of the eukaryotic cell). The plastids (the chloroplasts for example) were also independent organism. In consequence, in every cell, we have DNA in the nucleus and DNA in the mitochondria. The mitochondria is contained in every cell of our body and is transmitted via the ovule (and not the spermatozoid) to the offsprings.

Now let's think about your hypothesis that one of our organ (let's say, our liver) might have been an independent organism in the past. Therefore, this organ would contain different DNA than the rest of the cells of our body. How would you transfer the DNA of your liver to your offspring? Well, it is hardly imaginable.

Moreover, it has been argued that because we now have a complex and efficient immune system, a endosymbiose would be very unlikely.

But no, none of the cell in our body come from a previously different organism. But every cell of our body is some kind of chimera of two previous cells. Note: the vast majority of our DNA are present in the nucleus and not in the mitochondrion.

For more information about endosymbiose, have to look to this and this (wiki articles)

It seems much more easy to have two organisms that stay together during reproduction when reproduction is mediated by striking.

You may find some funny examples (border cases) of two organisms that don't separate during reproduction in corals (zooxanthella), leafcutter ants (and their fungus), parasitoid bees (and the virus that females create in their ovary) and lichens