On aggregate year to year Harper has increased science funding in a manner consistent with the liberals. This means that under Harper, we have had the highest levels of science funding in Canadian history.

Not if you add context. Accounting for inflation, granting council funding is down across the board, as much as 10% since 2007. Just because the amount of money is at a high point does not mean the rate is the same, and does not even really mean much when you consider that basically any sitting PM would be presiding over the "highest levels of science funding in Canadian history" since the funding almost always goes up each year. By this chart every PM since 1999 has had the highest level of science funding, again, context.

In terms of actual censorship there has been no effort to prevent scientific research from taking place, or being published.

Debatable. A not insignificant number of government scientists polled had said they felt pressure to alter or omit research. Reducing access to scientists is also bad because lots of government funded research either won't get reported on or will not be reported on properly because of no context being available from the scientists who did the studies. Censorship isn't black and white, with scientists either publishing or being prevented from publishing; the majority here is in the form of reporting.

Just because Harper is a consistent micromanager doesn't excuse it or make it right.