this prevents information loss but results into array of arrays

use strict;
use warnings;

use Data::Dump qw/pp/;

my $data_str= do { local $/;<DATA>};
$data_str=~ tr/{}/[]/;

print $data_str;

my $h;
eval "\$h =$data_str";
pp $h;

__DATA__
{
  alpha => {
    beta => {
      gamma => "theta",
      delta => "lambda",
    },
    beta => {
      gamma => "zeta",
    },
  },
}
[download]

Output:

[
  alpha => [
    beta => [
      gamma => "theta",
      delta => "lambda",
    ],
    beta => [
      gamma => "zeta",
    ],
  ],
]
[
  "alpha",
  [
    "beta",
    ["gamma", "theta", "delta", "lambda"],
    "beta",
    ["gamma", "zeta"],
  ],
]
[download]

now you can parse the data and tranform it to the structure you want. Note that I needed to quote the barewords in your original example!

UPDATE

If you just need a compact format, why don't you use YAML?

these are equivalent:

#YAML
---
- alpha:
    - beta:
        - gamma:
            - theta
        - delta:
            - lambda
    - beta:
        - gamma:
            - zeta
# PERL AoH³
[
  {
    alpha => [
          { beta => [{ gamma => ["theta"] }, { delta => ["lambda"] }] 
+},
          { beta => [{ gamma => ["zeta"] }] },
        ],
  },
]
[download]