Just because a party has defections doesn't mean the party is badly organized. One defection out of 94 members also isn't exactly a party not keeping together, especially if that defection comes from a member that lost her bid for power. If the party really was falling apart, you would have seen full-fledged splits already, long before the election. The AfD has a larger share of the vote then the Greens (Exists since 1980), The Left (2007) or FDP (1948) ever received.
I won't surprise anyone when I say I strongly oppose the platform of the AfD and seriously question some of their statements and statements of their (elected) members. But to simply ignore it on the basis of bad results (Outwinning every other third party in Germany's modern history), bad organization (One defection out of 94 members because of a leader dispute) or because they probably won't be able to achieve much in their opposition role (ignoring the fact that parties can and do influence eachother and the politics of their country without ever holding office) is to deny facts. Worse, it will only create more resentment from AfD-voters, a majority of whom state they did not vote because of the AfD platform but as a way to protest and influence Merkel. These are voters that gladly will vote CDU again after it re-aligns to a more conservative political positioning.
But don't forget, another large group of protest voters are from Die Linke, which used to be THE party of the anti-Wessie-esthablishment. In fact, in percentage, die Linke lost far more votes to the Afd (about 10%) then the CDU (5%). While the CDU will work to regain disappointed conservative voters from the west, Die Linke will do the same in the east. Both will become more socially conservative, tougher on immigration and more nationalist in nature.
So will the AfD see a decline in votes in 2021? Yes, probably, because the CDU/CSU, and in fact, the whole of German politics, will have re-aligned to appeal to those voters. The CDU cannot move to the crowded German left, so what else could be their strategy? Add to that the fact that Merkel will probably be replaced by a new face for that election. My money is on a candidate who will stay just clear of openly criticizing Merkel but never miss an opportunity to express his or her regret for the mistakes made 'by the government' in that period. Besides, during the next election, the AfD will have to either find a really good reason to campaign with continued 'principled opposition' or change its platform to include the possibility of entering the government - which means working with their political rival, the CDU and letting go of their strong anti-esthablishment views.