It's quite normal for dynamic resizing operations--and particularly shrinking--to take a long time. Files are spread across much, and perhaps most, of the original partition. They have to be re-pieced together to fit them in a smaller space, and the information about where their pieces exist has to be updated. If you are also having the partition automatically converted from FAT32 to ext2, that may take a while as well, as the files are stored somewhat differently.
If it takes more than a day, then I would start thinking there was something wrong.
As for whether or not it's OK to run your hard drive at near its maximum capacity for reads and writes, for hours at a time: yes, this is fine. Your hard drive is, among other things, a mechanical device, so the more it's used, the higher the likelihood of mechanical failure. But all hard drives fail eventually, and there's no reason to expect this one will fail any sooner, just because it runs heavily for hours.
Of course, if it's getting too hot, that is a problem. A properly constructed computer should never allow this to happen, even if the hard drive is reading and writing at 100% capacity for days, weeks, or months without interruption. (Depending on what hard drive you've purchased, running it like this for months might or might not bring about very early failure.) But if you find it is hot, and you're able to cool it with externally applied ventilation, that should be fine.
I don't mind losing the data,but the hard disk is really important.
If you have to cancel the operation, click Cancel. Really anything except cutting power to your computer or to the drive, won't physically damage the drive. Shutting down the operating system, using any method of harshness less than or equal to REISUB, will not be a problem. Even cutting power to the machine is unlikely to cause any real damage, although I would definitely avoid it when possible.
However, you may want to rethink the value you put in a single drive. All hard drives fail eventually, you can't prevent them from failing, and you can't prevent some of them (essentially selected at random) from failing long before you would expect them to fail. Some drives last longer than others (for some uses), and some drives are less likely to fail "early," but hard drives are replaceable (even in laptops) for a reason.
To put it another way: Hard drives' lifetimes are limited, so much so that in any computer where some other component fails first, the computer's craftsmanship should be questioned.