The model of EI is that the therapist can either work directly with you and your child if the child tolerates it, but she/he can also instruct you in what you need to do to help your son. So, if the child doesn't do well with others (totally normal for some 16 month olds!) then you can complete the work without the therapist actually handling the child. This might only last a session or two, until trust is built or re-built, in this case.
Hopefully, in time with this "hands off" approach, your child may warm to this therapist again. She/he can use a doll to demonstrate what you can do with your son, while you are all on the floor together playing. Sometimes, a simple warm up of a few favorite songs, ring-around-the-rosy, or dancing to music on the CD player can get the session off to a good start. I am guessing that she already uses cool toys and activities that capture his attention? Bubbles, balls, silks for parachutes, blocks, trucks, etc?
All activities should be meaningful and engaging to your child, at whatever age he is at the time. A child really should not have to "power through" anything. They may need to work harder than they are used to, but the work should be in the context of their play and the therapist should be skilled in ways to engage your son in activities that encourage him to use the correct muscles without him really knowing that he is working!
A pool, if you have access to one, is a great way to get a ton of work done in a fun environment. The therapist can meet you at a YMCA for one session to show you what to do. Or, there are some clinics with pools with specialized aquatic P.T's that also accept EI funding. Your service coordinator would just need to add an authorization for "Aquatic Physical Therapy." This is a common addition to the home-based therapy sessions.
Email me if you have anymore questions. I am happy to help!
(As a last resort, you can always change therapy providers to find someone who may be a better fit. But, it sounds like you like the P.T., so talk with her about how she might be able to make your child more comfortable. Sometimes, just changing the location works. Like, meet up at a park, library or other interesting setting, even McDonald playlands work great! But, if it is not working after a few more weeks, call your service coordinator and explain the situation. Good luck!)