Let's consider his options:
1) Simply allow defunding in the CR and extend the CR by a year and in return extract major concessions on everything else
2) Fight the Ted Cruz faction of the senate over THIS issue
Now ask yourself which path Reid would choose if he thought defunding wouldn't affect PPACA rollout. I believe he would use the opportunity to extract concessions on the sequester, taxes, and medicaid. He would also send billions more to progressive supporters (Solyndra), and let Obamacare go on unaffected. The internecine fighting would still go on within the Republican party and eventually Cruz's plan would be shown as a failure and Boehner would emerge as a weakened leader who already agrees to conceded any time he is given the opportunity. Cruz and other fighters would be permanently marginalized as passionate but ineffective.
If however Reid believes that defunding is a viable path then he would put all the other priorities aside to pursue one thing - securing money for a boondoggle of a program (that has probably already run through more money than has been allocated for it).
Which path has Reid chosen? What does that say?