Delete default configuration files from cluster checks runner

[celenechang]

What this PR does / why we need it:

Rather than delete the entire conf.d folder, only delete the configuration for checks enabled by default.

Currently, this list is

# find /etc/datadog-agent/conf.d/ -name "*.yaml.default" -type f
/etc/datadog-agent/conf.d/cri.d/conf.yaml.default
/etc/datadog-agent/conf.d/network.d/conf.yaml.default
/etc/datadog-agent/conf.d/container_image.d/conf.yaml.default
/etc/datadog-agent/conf.d/io.d/conf.yaml.default
/etc/datadog-agent/conf.d/ntp.d/conf.yaml.default
/etc/datadog-agent/conf.d/containerd.d/conf.yaml.default
/etc/datadog-agent/conf.d/kubelet.d/conf.yaml.default
/etc/datadog-agent/conf.d/sbom.d/conf.yaml.default
/etc/datadog-agent/conf.d/file_handle.d/conf.yaml.default
/etc/datadog-agent/conf.d/cpu.d/conf.yaml.default
/etc/datadog-agent/conf.d/ecs_fargate.d/conf.yaml.default
/etc/datadog-agent/conf.d/orchestrator_ecs.d/conf.yaml.default
/etc/datadog-agent/conf.d/orchestrator_pod.d/conf.yaml.default
/etc/datadog-agent/conf.d/container.d/conf.yaml.default
/etc/datadog-agent/conf.d/memory.d/conf.yaml.default
/etc/datadog-agent/conf.d/load.d/conf.yaml.default
/etc/datadog-agent/conf.d/container_lifecycle.d/conf.yaml.default
/etc/datadog-agent/conf.d/uptime.d/conf.yaml.default
/etc/datadog-agent/conf.d/eks_fargate.d/conf.yaml.default
/etc/datadog-agent/conf.d/telemetry.d/conf.yaml.default
/etc/datadog-agent/conf.d/service_discovery.d/conf.yaml.default
/etc/datadog-agent/conf.d/disk.d/conf.yaml.default
/etc/datadog-agent/conf.d/docker.d/conf.yaml.default

Which issue this PR fixes

(optional, in fixes #<issue number>(, fixes #<issue_number>, ...) format, will close that issue when PR gets merged)

• fixes #

Special notes for your reviewer:

Checklist

[Place an '[x]' (no spaces) in all applicable fields. Please remove unrelated fields.]

• [X] Chart Version bumped
• [X] Documentation has been updated with helm-docs (run: .github/helm-docs.sh)
• [X] CHANGELOG.md has been updated
• [X] Variables are documented in the README.md