Both kernels are fine. 2.6.8 is more modern thus supports more modern hardware, 2.4.27 includes support for some old hardware that nobody cares about to port to 2.6 (an example:my dxr3 hardware mpeg decoder is not ported to 2.6 yet).
2.4.27 has slightly better throughput on single processor systems with medium load. 2.6 has better throughput on multi-processor systems on high load.
It is possible to install both later and choose which to boot with GRUB.
I recommend 2.6.8 because of udev. It's so great to do ls /dev and only see device nodes for devices actually present on your system.
BTW. the installer is perfectly capable of wiping the whole disk. You should probably read the installer manual at
http://www.debian.org/devel/debian-installer