I saw this same thing too, but the new figures Hoth Luke, Hoth Droid, Tatooine wave, etc. ring up with the higher $4.99 price point. AND, the cartoon figures still ring up at the new $6.99 price.
However, the new 2003 and/or recarded 2003 figures which still have the old UPC combo (like Ack-Med Beq or the recarded figures Han/Fett/Ani) however, will USUALLY ring up at the clearance price (there are always exceptions, based on the UPC).
The reason that Targets are putting the "older" figures (anything from 2003 Saga Collection 1 and Collection 2) on clearance is because both the 2004 figure assortments and the Clone Wars cartoon figures both have new assortment numbers.
In other words, in terms of shelf space, the 04 figure assortment is replacing Collection 1 and the Cartoon figures are replacing Collection 2. This is standard Target procedure when Hasbro starts shipping them items with a new assortment number.
All it means is that Target is NOT expecting anymore 2003 collection 1 and 2 (2003) figures from Hasbro. They do however have product in the DC still to be shipped to stores though...
It is NOT a sign that Target will stop carrying SW figures! (I hate those "clearance = no more SW at store X" rumors that always start up).
I guess it is to our benefit that Target still sorts/stocks by assortment and Hasbro is selling mixed cases at the start of the year. Target will get in a "new" case of 2004 figures, but any 2003 repack figures will ring up at the clearance prices!
So, keep an eye out at Target, you'll probably see "new" figures like Dignitary #2 or Ack-Med Beq dirt cheap after Christmas, however the others (like the new 2004 figures) will stilll be $5!