Unless you're a traffic engineer, then neither you nor I are qualified to second guess the reason(s) why the yield sign was removed. More often than not, "engineering decisions" (and so long as they are not likely to lead to any unsafe conditions/traffic violations) do allow for some leeway in what "guidance" is followed to install or remove a sign.
I posted that link as a way for you to check whether the "traffic light" (not the "yield sign") is properly posted/positioned and that it is not obstructed... But I'll still oblige you with my own analysis of what is stated in the manual. let me refer you to Section 2B.04 (which starts on page 49)... Now scroll down to the bottom of page 50 (and you'll see the following):
Standard:
Because the potential for conflicting commands could create driver confusion, YIELD or STOP signs shall not be used in conjunction with any traffic control signal operation, except in the following cases:
A. If the signal indication for an approach is a flashing red at all times;
B. If a minor street or driveway is located within or adjacent to the area controlled by the traffic control signal, but does not require separate traffic signal control because an extremely low potential for conflict exists; or
C. If a channelized turn lane is separated from the adjacent travel lanes by an island and the channelized turn lane is not controlled by a traffic control signal.
As you can see, it is clearly stated that a "YIELD .... signs shall not be used in conjunction with any traffic control signal operation" unless (one of the conditions is: "a channelized turn lane is separated from the adjacent travel lanes by an island and the channelized turn lane is not controlled by a traffic control signal".
My interpretation of that is as follows: There is in fact a traffic signal (the red light you mentioned in your post)... That on its own means that a yield sign SHALL NOT be posted... Additionally, the fact (as you stated) that the turning lane is NOT separated from the adjacent traffic lanes by an island, would be another reason why a Yield sign should not be posted.
Legally speaking, you were cited for failing to make a complete stop before proceeding through a red light. Accordingly, the element that must be proven by the prosecution is your "failure to stop". As has been stated a number of times here, the fact that there used to be a yield sign is not a valid defense to the alleged violation that you committed at the time and place that you committed it. So while you can only hope for a sympathetic judge who may give you a break, you should keep in mind that he/she is neither required nor obligated to do so. (See the "tough luck" story that wertach posted).
Good luck!

