Yep, I got your private email. Thanks for posting it to the forms.
You could add the activation to your .bashrc file, so that it loads automatically when you connect to the server. That saves the first step. Also, you only have to run 'source deactivate' if you are switching to a different conda environment, so that could save the final step too.
Yeah, conda was never designed to be a 'one step' solution. Before using software in a conda environment, you do have to activate it. Even worse (or better!) every user has to install their own conda environments. So if someone else is using your pipeline on a different account, they would also have to install qiime, as shown here.
I quite like this flexibility, but it's a lot more work for new users compared to 'module load qiime'