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While cultural (and eventually genetic) differences would likely develop over time were the colonists on mars completely isolated from earth culture and genes from earth, I don't find that scenario likely.
Establishing a colony on Mars would be a massive undertaking, logistically speaking. Barring significant advances in many fields, the colony would remain reliant upon Earth for a number of things.
Furthermore, given conditions on Mars, it's not something that we would be likely to undertake just for its own sake; the colony would be established primarily for research, with mining (assuming sufficient concentrations to warrant the cost of shipping it) and goods production (taking advantage of conditions on mars vs those on earth, and making the same cost-benefit assumptions re: mining). As such, I would expect the colony to remain more or less in constant contact with earth, and most likely there would be somewhat regular arrivals and departures to and from earth.
Given all that, I expect that cultural and genetic drift would be minimized, if present at all. This would prevent the colony from becoming aliens in respect to their compatriots on earth.
Total isolation of the colony is extremely unlikely, but were it to occur without also killing off all the colonists, I would expect cultural differences to arise within a few generations, but still not genetic ones. Remember- genetic drift is slow, and faster changes are almost always in response to selective pressure, and the selective pressure on prospective colonists would not be from Mars' conditions, but rather from the earth-like conditions created for them to survive under; we're already quite well suited to these conditions, so I wouldn't expect much in the way of genetic change for a very, very long time, and only at the somewhat random whims of genetic drift.
Now, the colonists on mars would be alien insofar as any life on mars is concerned, but is that meaningful or relevant in the absence of sentient or even large-scale life? I took the debate to be referring to them being aliens in respect to humans, as being alien in respect to martians would seem to require some martians.
Final answer: Possibly, but most likely No.