I guess it depends how you define systemic corruption, but I disagree with your statement above.
No, I don't believe there's a secret cabal of guys in a back room plotting to facilitate doping, but I do think the organization is structured in a way which discourages thorough investigation and sanction, and encourages portraying a clean sport above truth. There's a mountain of evidence to support this position: the Vrijman report, the lack of follow-up on the Astana transfusion kits, the Postal garbarge hunts, the current silence over the plasticizer test results (not just for Contador, but for everybody).
The bottom line is that the organization is structured to both promote and regulate the sport, and where doping is concerned this is going to result in a governing body with competing interests; hence corruption becomes almost impossible to avoid. So, I'd would say that it is, indeed, "organizational".
My basic thoughts on how to change this are to do the following:
-incorporate the UCI in a country where it would actually be accountable to the rule of law. I don't know where, but Switzerland is not that country
-remove the federations and the UCI completely from testing, results management and sanctions
-completely re-do the testing punishment structure to include all parties involved (directors, staff, sponsors, national federations), not just riders.
Until these steps are taken, I'll only view the corruption within the sport's governing body as "organizational".