Containers are completely orthogonal to the cloud vendor lock-in issue. You still can consume proprietary services and APIs from containers just like you may use them from VMs.
All containers give you, is a portable omnibus image format. Container Orchestration software like Mesos/Marathon or Kubernetes gives you ability to deploy and schedule containers.
For those who want to be truly multi-cloud, they need to exercise high level of self-discipline, periodically doing code and devops scripts reviews and audits and check their system on different clouds or on-prem.
I.e. in short they shouldn't take any shortcuts, but IMO for startups taking shortcuts is preferred way.
