This article is worth closer attention.
First, let us not be stupid and think that the whole samurai class was descended from a unique race. Please read this short
history of the samurai. The samurai class only appeared during the Heian Period (794-1185) and were basically mercenaries, with some of them recruited among farmers.
As the very first samurai were recruited to fight th Ainu in Northern Honshu, I believe it is possible that
some Ainu may have :
1) defeated some samurai, taken their weapons and pretended being samurai themselves (for the pay, or to avoid being killed later). Or alternatively, some Ainu were very intelligent and successfully pretended to be samurai to avoid being killed or discriminated against (could that strange errant guy in Kurosawa's movie The Seven Samurai be an Ainu who managed to pass for a Samurai and slowly became accepted as one ?).
2) raped or intermarry with Japanese women, whose descendants may have become samurai in Northern Honshu (not knowing about their own Ainu origins)
3) On the contrary, Japanese samurai have surely raped many conquered Ainu women, and may have taken a few as wives or concubines, which explains the partially Ainu blood of their descendants.
4) some defeated Ainu were eventually recruited as samurai themselves (like in the movie The Last Samurai).
It is anyway undeniable that the early samurai (who didn't have the elaborate armour and bushido code, nor the class recognition that all appeared later) had very close and frequent contacts with the Ainu, which can only increase the chances of the abobe-mentioned occurances.
It is therefore possible that a few of these early samurai had Ainu blood, and later, when the samurai class became dominant, spread their genes much more "profusely" than the average, poor Japanese farmers.
It would be interesting to compare the fate of the Ainu to that of the Celtic people in Europe. The Celts once controlled an area spreading from Spain to Central Europe, via France, Belgium, Britain, Ireland and North Italy. However, the Celts were conquered by the Romans and forced to speak Latin, intermarry with the Romans and adopt Roman customs. After came the Germanic tribes who invaded all the Western Roman Empire. Although these tribes adopted Latin as an official language (except in England), they became the dominant class in all these countries and mixed with the local Celto-Romans.
But some areas remained predominantly Celtic, like North-Western Spain (Galicia, Asturias...), little Brittany in France, and Wales, Cornwall and the Scottish Highlands in Britain. With time, they all came to speak Spanish, French and English with only very few people still speaking Gaelic and practising Celtic customs nowadays (Wales was the most successful to preserve its culture). However, these people mixed very little with the "invadors" and retain most of the Celtic genes to this day, although they are completely integrated to their country's society and they might not know themselves about their Celtic roots.
Many of these Celts (especially from Britain and Ireland) migrated to America, where they once again adopted the local culture, language and customs. Interestingly, these Irish and Scottish migrants have become among the most successful Americans, with a sizeable proportion controlling the country. Just see all the name in "Mac
Something" (MacDonald, MacAlister, etc.), and all the Irish presidents or famous politicians (Kennedy, Reagan, Nixon, Kerry...). An estimated 45 million American have Irish roots (don't know of Scottish or Welsh), and about half of the Australians can also claim Irish or Scottish ancestors (with many only partly Irish/Scottish of course, due to intermarriages). So, although the Celts have lost most of their language and culture, they have survived and well in modern society. Could it be the same with the Ainu, to a much lower extent ? Some Japanese do look different (slightly more Caucasian) than other Mongoloid people. For example Abe Hiroshi (who we often see in TV commercials) :