wrangler generate modifies formatting of wrangler.toml

### 🐛 Bug Report

#### Environment

* operating system: macOS Mojave 10.14.6
* output of `rustc -V`: rustc 1.35.0 (3c235d560 2019-05-20)
* output of `node -v`: v11.11.0
* output of `wrangler -V`: wrangler 1.8.0-rc.1

#### Steps to reproduce

Run `wrangler generate my-crl-worker https://github.com/cloudflare/access-crl-worker-template`

This project has an empty `wrangler.toml` file that looks like this.
```
name = "access-crl-worker"
type = "webpack"

workers_dev = false
route = ""
account_id = ""
zone_id = ""
kv-namespaces = [{ binding = "CRL_NAMESPACE", id = "" }]
vars = { CRL_URL = "" }
```

#### What did you expect to see?

I expected to see what was in the `wrangler.toml` file in the template repo.

#### What did you see instead?

I got a slightly different version of the `wrangler.toml` file

```
name = "access-crl-worker-test"
type = "webpack"
account_id = ""
workers_dev = true
route = ""
zone_id = ""

[[kv-namespaces]]
id = ""
binding = "CRL_NAMESPACE"

[vars]
CRL_URL = ""
```

In my opinion, the new version is better. It was just unexpected.