CPU is running a bit hot, can I still use it til I receive new cooler?

A typical full-load temperature for IB on stock cooler is 65-75C, 50C is a non-issue.

You are below normal temps. I wouldn't even worry about spending money on a different cooler. You are no where near a temperarture threshold, it appears.

50c if at idle is high, all the heatsink legs clamped down?

BIOS temperatures are often higher than idle temperatures with an OS loaded because the BIOS uses a busy loop instead of low-power sleep states like an OS' per-core idle loops do.

50C in the BIOS is definitely too high (not "true" idle in the BIOS, but it should still be lower than 50C). I agree with das_stig's assessment that it sound's like the HSF isn't seated well. Check the pins, and if you can easily pull any of them out without unlocking them, it's not correct.

Agreed, but 50C in the BIOS is too high, regardless.

It's seated appropriately. I had some trouble with the thermal paste that might be the problem... I had to reapply new stuff because I got interrupted the first time I started building, but the stuff I got was more of a clay than a paste so it didn't spread well and probably isn't thick enough. I just ordered the CM 212+ and some Arctic 5. In the mean time, can I still use my computer without damaging it?

As long as you're not constantly at something like 80C+, you'll be fine.

IB does have a reputation for running around 10C hotter than previous Core CPUs of a given TDP.

You should download a program to monitor CPU temperature from the OS rather than BIOS. On my PC (C2D-E8400), I get 45C from BIOS, 33C idle under Windows, 55C at full-load... BIOS temperature is about half-way between Windows idle and full-load.

What matters is the temperature under your typical load with an OS loaded, not temperature readout in BIOS. At 50C, you are nowhere near Ivy Bridge's 105C thermal limit.