The decision to use different fuels for the main engine and the RCS was made before contractors were assigned, back when various NASA centers were conducting feasibility studies. At the time, the mission mode was expected to be a direct descent to the moon in one spacecraft. The main propulsion was expected to be solid rocket motors!
188.8.131.52 Service propulsion system. Early requirements for the service module included vernier and main propulsion systems for a direct lunar landing profile. The main propulsion system was to consist of several identical solid-propellant motors which would provide thrust for translunar abort and lunar ascent. A separate module was to be designed that would provide for terminal descent. These requirements were changed early in 1962 to specify a single service module engine. Earth-storable liquid hypergolic propellants were to be used by the new system, which could include single or multiple thrust chambers. The service propulsion system was to be capable of providing for abort after jettison of the launch escape system, for launch from the lunar surface, and for midcourse corrections during earth return.
Apollo Program Summary Report
This is also confirmed in The Apollo Spacecraft: A Chronology:
The Group for Onboard Propulsion reviewed the three contractors' work on the Apollo feasibility studies. Among studies being undertaken by the NASA Centers and reported on at this meeting were: an STG consideration of an all-solid fuel propulsion system for a circumlunar flight, determination of midcourse and abort propulsion system requirements based on Saturn trajectories (MSFC), experimental evaluation at zero gravity of expulsion bag techniques for cryogenic propellants (Lewis), analysis and experiments on solid propellant rocket motors of very high mass fraction (Langley), methods of achieving thrust vector control by secondary injection of gases and the design of a highly reliable and versatile bipropellant spacecraft propellant system using hydrogen tetroxide and hydrazine or hydrazine derivatives (JPL), and a contract to examine hardware requirements for space missions and lunar landings (NASA Headquarters).
1961 January 6
By 1961 November 27, main propulsion was changed to a not-yet-specified hypergolic propellant. However, RCS development was already progressing along a separate path:
A single-engine service module propulsion system would replace the earlier vernier and mission propulsion systems. [...] Earth-storable, hypergolic propellants would be used by the new system, which would include single- or multiple-thrust chambers with a thrust-to-weight ratio of at least 0.4 for all chambers operating (based on the lunar launch configuration) and would have a pressurized propellant feed system.
The reaction control systems for the command and service modules would now each consist of two independent systems, both capable of meeting the total torque and propellant requirements. The fuel would be monomethylhydrazine and the oxidizer would be a mixture of nitrogen tetroxide and nitrous oxide.
The change to a lunar orbital rendezvous didn't occur until 1962 July 11. By then, too much work had been put into the two engine systems to justify consolidating their fuel.