The appropriate way would be to:
- Make a jig out of wood that will hold the pipe to be drilled
- The jig could be flat or have the desired 45° angle built into it.
- Building it flat allows it to be used for drilling holes into pipe at any desired angle in the future, making it more useful
- Clamp the jig to the table of a drill press.
- Either have the drill press table level (for a jig with the angle built in) or tilt it to 45° (for a "flat" jig).
- Drill the hole with an appropriately sized bit.
- I would use a hole saw from a set with a replaceable pilot bit.
- Replace the supplied bit with a long one that will reach the pipe before the edge of the cutter will reach it.
- Use the long pilot bit to ensure that the center of the hole is where you want it to be.
A hole-saw set like this:
image courtesy of lowes.com. No endorsement intended or implied
Has a pilot bit that can be replaced. Simply purchase a longer bit that will fit so that the pilot bit hits the pipe before the larger cutter hits, like this crude drawing:
image courtesy of lowes.com. No endorsement intended or implied. Edited by me.
Where the red line indicates the pipe and the blue line indicates the longer drill bit.
This is the kind of drill press (or "pillar/post drill" as it's called in some countries) I'm referring to. This model has a 10" (254mm) capacity between the the chuck and the lowest position of the table:
Image courtesy of HarborFreight.com customer review. Note that this shows it sitting on the floor, not yet installed on a bench top. Click to embiggen.