Clean up noisy warnings encountered in normal work flows

[mhodson-rigetti]

Pre-Report Checklist

• I am running the latest versions of pyQuil and the Forest SDK
• I checked to make sure that this bug has not already been reported

Issue Description

This issue is to remove noisy warnings encountered during normal work flows. The first example is the warning about proving the QPUCompiler with native QUIL, without going through quilc, which is a normal flow when generating native circuits.

Other warnings across the code base should be checked.

How to Reproduce

p = Program()
p.inst(RX())

qc.compiler.native_quil_to_executable(p)

The intervening output to be removed are warning log messages.

Environment Context

Unspecified.