We have a Drivers WDC and a contructors WCC for a reason. If the team work well for the driver (and with him), they deserve a great result in the WCC.
Why should the driver get affected by the operational failures of his team? He's got a WDC to shoot for, and no doubt he needs his team for it but his efforts should not be affected by the mistakes of his team (who are vying also for the WCC).
Why should the "team" get affected by poor driving choices of the driver? They've got a WCC to shoot for, and no doubt they need their driver for it but their efforts should not be affected by the mistakes of their driver (who is vying also for the WCC).
Same sort of penalties as now depending on the crime, reprimand, drive through, grid penalty, time penalty, points deduction, race ban.
This smacks of double-standards. In this case, the team suffers as well as the driver, but you don't want the same thing the other way round. How is this possibly a fair outcome?
There are other issues, too.
Suppose the team runs an illegal component on their car during qualifying which gives them a significant advantage over the other teams, and their driver qualifies on pole position as a result. During scrutineering, the part is discovered, and under current rules the car would be declared illegal and the driver's times erased from the session. Now, the driver did not make the decision to run this component, but if you view the team and driver as separate entities then the driver suffers for the team's mistake. You could just dock the team WCC points, but is this fair on the competition? After all, the guy on pole is there because of an unfair advantage, so this is going to cause issues with other teams.
On the other hand, let's say one driver intentionally collides with another during the race (I'm sure we all know who I'm talking about here). Ideally, they should be black-flagged for dangerous driving, in which case (viewing team and driver as separate again) the team would suffer for something totally out of their control (unless the team boss is Flavio Briatore, in which case that's not certain...). But could you really just dock the driver WDC points and leave someone like that out on the track?
Overall, things should balance out, as in some cases one party will suffer from the actions of the other, and in others the reverse will be true. By taking the win as a team, lose as a team approach, you should more or less achieve a balance (although in cases where you have a massively incompetent pit crew or driver, this may not necessarily be true, but such cases should be pretty rare).